From efae6da6da4192b6dc1dcc187bfde9d961a2fcce Mon Sep 17 00:00:00 2001 From: Jonn Smith Date: Tue, 2 Aug 2022 13:58:02 -0400 Subject: [PATCH] Added `tagfix` command to correct position tags post-alignment and other minor updates. (#144) - Added `tagfix` command to update reads after alignment. - Added documentation for `tagfix`. - Changed Slide-seq `XQ` tag to `XR` to prevent `XQ` tag from being overriden. - Other minor updates. --- docs/commands.md | 1 + docs/commands/tagfix.md | 37 +++ docs/commands/train.md | 2 +- docs/commands/version.md | 2 +- docs/faq.md | 64 ++--- src/longbow/inspect/command.py | 2 +- src/longbow/pad/command.py | 2 +- src/longbow/tagfix/__init__.py | 0 src/longbow/tagfix/command.py | 212 +++++++++++++++++ src/longbow/utils/bam_utils.py | 23 +- src/longbow/utils/constants.py | 2 +- src/longbow/utils/model.py | 11 +- tests/integration/test_tagfix.py | 80 +++++++ .../mas_15_spatial_slide-seq_single_none.json | 4 +- .../tagfix/tagfix_test_data.expected.sam | 224 ++++++++++++++++++ tests/test_data/tagfix/tagfix_test_data.sam | 221 +++++++++++++++++ 16 files changed, 838 insertions(+), 49 deletions(-) create mode 100644 docs/commands/tagfix.md create mode 100644 src/longbow/tagfix/__init__.py create mode 100644 src/longbow/tagfix/command.py create mode 100644 tests/integration/test_tagfix.py create mode 100644 tests/test_data/tagfix/tagfix_test_data.expected.sam create mode 100644 tests/test_data/tagfix/tagfix_test_data.sam diff --git a/docs/commands.md b/docs/commands.md index 765eae42..e788057c 100644 --- a/docs/commands.md +++ b/docs/commands.md @@ -33,6 +33,7 @@ Commands: scsplit Create files for use in `alevin` for single-cell analysis. segment Segment pre-annotated reads from an input BAM file. stats Calculate and produce stats on the given input bam file. + tagfix Update longbow read tags after alignment. train Train transition and emission probabilities on real data. version Print the version of longbow. ``` diff --git a/docs/commands/tagfix.md b/docs/commands/tagfix.md new file mode 100644 index 00000000..5f40bca0 --- /dev/null +++ b/docs/commands/tagfix.md @@ -0,0 +1,37 @@ +--- +layout: default +title: extract +description: "Extract reads." +nav_order: 14 +parent: Commands +--- + +# Tagfix + +## Description + +Update longbow read tags after alignment. + +According to the SAM spec, aligners reverse-complement the read sequence in the event that a read maps to the reverse strand. +However, the aligners do not know about the tags that `Longbow` adds to the reads and therefore certain tags will be incorrect +for reverse-stranded reads after the alignment process (e.g. the `SG` tag). + +`Tagfix` checks each read in the input bam file for its strandedness and in the event of a reverse strand read, the position-based +tags that have been added to the read by `Longbow` are corrected to reflect the sequence of bases in the BAM file itself. + +## Command help + +```shell +$ longbow tagfix --help +Usage: longbow tagfix [OPTIONS] INPUT_BAM + + Update longbow read tags after alignment. + +Options: + -v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG + -t, --threads INTEGER number of threads to use (0 for all) [default: 7] + -o, --output-bam PATH annotated bam output [default: stdout] + -f, --force Force overwrite of the output files if they exist. + [default: False] + --help Show this message and exit. +``` diff --git a/docs/commands/train.md b/docs/commands/train.md index e94f2549..2b75f268 100644 --- a/docs/commands/train.md +++ b/docs/commands/train.md @@ -2,7 +2,7 @@ layout: default title: train description: "Train model." -nav_order: 14 +nav_order: 15 parent: Commands --- diff --git a/docs/commands/version.md b/docs/commands/version.md index 49ea140d..92321975 100644 --- a/docs/commands/version.md +++ b/docs/commands/version.md @@ -2,7 +2,7 @@ layout: default title: version description: "Print version number." -nav_order: 15 +nav_order: 16 parent: Commands --- diff --git a/docs/faq.md b/docs/faq.md index 3414c99c..a1bff97a 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -13,38 +13,38 @@ Longbow adds several tags to output reads to indicate various metadata features. the read tags added by each tool and what data they contain: | Read Tag | Type | Tool(s) | Description | -|:---|:---|:---|:---| -| YS | f | Annotate, Demultiplex | Longbow HMM model score (log probability) | -| SG | Z | Annotate, Demultiplex | Read segment information indicating the boundaries and labels of each segment in the read. For example: `SG:Z:random:0-53,Poly_T:54-85,cDNA:86-823,MARS:824-853,N:854-869,VENUS:870-894,CBC:895-910,UMI:911-920,Poly_T:921-951,cDNA:952-2030,MARS:2031-2060,O:2061-2076,VENUS:2077-2100,CBC:2101-2116,UMI:2117-2126,Poly_T:2127-2157,cDNA:2158-3747,MARS:3748-3777,P:3778-3794` | -| YN | Z | Annotate, Demultiplex | Name of the model used to annotate the reads | -| RC | i | Annotate, Demultiplex | 1 if the read has been reverse-complemented; 0 otherwise | -| XQ | Z | Annotate, Demultiplex | Comma-delimited quality scores ratios for each segment in a given read. Scores for random segments are set to 0/0. Scores for other segments are the optimal alignment score (Smith-Waterman) for the expected sequence over 2x the sequence length. For example: `XQ:Z:0/0,12/60,0/0,58/60,30/32,46/46,0/0,0/0,60/60,0/0,58/60,30/32,46/46,0/0,0/0,60/60,0/0,58/60,32/32` | -| YQ | f | Annotate, Demultiplex | Approximate read quality. Read quality is approximated by summing the individual segment scores and dividing that sum by the sum of the total possible (best) scores (as defined by the `XQ` tag). | -| ZS | i | Segment, Extract | 1 if the given read is segmented; 0 otherwise | -| YV | i | Filter | 1 if the given read is valid according to the expected order of the model segments; 0 otherwise | -| YK | Z | Filter | Name of the first valid adapter / named non-random region in the given read | -| YG | i | Filter | Number of valid adapters / named non-random regions in the given read | -| ZU | Z | Segment | Unique Molecular Identifier (UMI) sequence for the given segmented read | -| XU | i | Segment | Position (0-based) in the read of the first base in the annotated Unique Molecular Identifier (UMI) sequence for the given segmented read | -| CR | Z | Segment | Cell Barcode (CBC) sequence for the given segmented read | -| XB | i | Segment | Position (0-based) in the read of the first base in the Cell Barcode (CBC) sequence in the given segmented read | -| XF | f | Segment | Confidence factor for the Cell Barcode (CBC) in the given segmented read. The confidence factor is based on the quality of each base in the CBC and is given by the following: `scale_factor = 100 scale_factor * reduce(operator.mul, map(lambda q: 1. - 10 ** (-(ord(q) - 33.) / 10), qual_string))` | -| XA | Z | Segment | String containing the name of the tag containing the Cell Barcode (CBC) tag followed by the Unique Molecular Identifier (UMI) tag: `XC-XM` | -| X1 | Z | Segment | Sequence for Spatial Barcode 1 for the given segmented read | -| XP | i | Segment | Position (0-based) in the read of the first base in the Spatial Barcode 1 sequence in the given segmented read | -| X2 | Z | Segment | Sequence for Spatial Barcode 2 for the given segmented read | -| XQ | i | Segment | Position (0-based) in the read of the first base in the Spatial Barcode 2 sequence in the given segmented read | -| XM | Z | Segment | Raw Unique Molecular Identifier (UMI) sequence for the given segmented read (for IsoSeq3 compatibility) | -| XC | Z | Segment | Raw Cell Barcode (CBC) sequence for the given segmented read (for IsoSeq3 compatibility) | -| YC | i | Correct | True IFF barcode correction was able to be performed (including "correction" where the original barcode did not change). False otherwise. | -| YP | i | Correct | True IFF the barcode was able to be corrected AND the corrected barcode != the raw barcode. False otherwise. | -| ic | i | Segment | Sum of number of passes from all ZMWs used to create consensus. Always set to 1. (for IsoSeq3 compatibility) | -| im | Z | Segment | ZMW names associated with a given segmented read. Set to the name of the parent read for a segmented read. (e.g. `m64013e_211031_055434/1/ccs`). (for IsoSeq3 compatibility) | -| is | i | Segment | Number of ZMWs associated with a given segmented read. Always set to 1. (for IsoSeq3 compatibility) | -| it | Z | Segment | List of barcodes / UMIs tagged/clipped during segmentation (e.g. `it:Z:CATTAGGTCATCCCTA,AAATTTTGGA`) (for IsoSeq3 compatibility) | -| zm | i | Segment | ZMW number from which the given read originates. (for IsoSeq3 compatibility) | -| XN | Z | Segment, Extract | Altered read name given by Longbow to a segmented read (used for debugging). This name consists of the original read name followed by the start and end positions of the segment on the original read, then the names of the bounding adapters / known regions. For example: `XN:Z:m64013e_211029_235558/24/ccs/0_1960/START-MARS` | -| pz | i | Correct | Offset of the new, corrected, barcode/tag relative to the original, raw value (0-based). NOTE: if the tag could not be corrected, this tag is not present in the output read. | +|:---------|:---|:---|:---| +| YS | f | Annotate, Demultiplex | Longbow HMM model score (log probability) | +| SG | Z | Annotate, Demultiplex | Read segment information indicating the boundaries and labels of each segment in the read. For example: `SG:Z:random:0-53,Poly_T:54-85,cDNA:86-823,MARS:824-853,N:854-869,VENUS:870-894,CBC:895-910,UMI:911-920,Poly_T:921-951,cDNA:952-2030,MARS:2031-2060,O:2061-2076,VENUS:2077-2100,CBC:2101-2116,UMI:2117-2126,Poly_T:2127-2157,cDNA:2158-3747,MARS:3748-3777,P:3778-3794` | +| YN | Z | Annotate, Demultiplex | Name of the model used to annotate the reads | +| RC | i | Annotate, Demultiplex | 1 if the read has been reverse-complemented; 0 otherwise | +| XQ | Z | Annotate, Demultiplex | Comma-delimited quality scores ratios for each segment in a given read. Scores for random segments are set to 0/0. Scores for other segments are the optimal alignment score (Smith-Waterman) for the expected sequence over 2x the sequence length. For example: `XQ:Z:0/0,12/60,0/0,58/60,30/32,46/46,0/0,0/0,60/60,0/0,58/60,30/32,46/46,0/0,0/0,60/60,0/0,58/60,32/32` | +| YQ | f | Annotate, Demultiplex | Approximate read quality. Read quality is approximated by summing the individual segment scores and dividing that sum by the sum of the total possible (best) scores (as defined by the `XQ` tag). | +| ZS | i | Segment, Extract | 1 if the given read is segmented; 0 otherwise | +| YV | i | Filter | 1 if the given read is valid according to the expected order of the model segments; 0 otherwise | +| YK | Z | Filter | Name of the first valid adapter / named non-random region in the given read | +| YG | i | Filter | Number of valid adapters / named non-random regions in the given read | +| ZU | Z | Segment | Unique Molecular Identifier (UMI) sequence for the given segmented read | +| XU | i | Segment | Position (0-based) in the read of the first base in the annotated Unique Molecular Identifier (UMI) sequence for the given segmented read | +| CR | Z | Segment | Cell Barcode (CBC) sequence for the given segmented read | +| XB | i | Segment | Position (0-based) in the read of the first base in the Cell Barcode (CBC) sequence in the given segmented read | +| XF | f | Segment | Confidence factor for the Cell Barcode (CBC) in the given segmented read. The confidence factor is based on the quality of each base in the CBC and is given by the following: `scale_factor = 100 scale_factor * reduce(operator.mul, map(lambda q: 1. - 10 ** (-(ord(q) - 33.) / 10), qual_string))` | +| XA | Z | Segment | String containing the name of the tag containing the Cell Barcode (CBC) tag followed by the Unique Molecular Identifier (UMI) tag: `XC-XM` | +| X1 | Z | Segment | Sequence for Spatial Barcode 1 for the given segmented read | +| XP | i | Segment | Position (0-based) in the read of the first base in the Spatial Barcode 1 sequence in the given segmented read | +| X2 | Z | Segment | Sequence for Spatial Barcode 2 for the given segmented read | +| XR | i | Segment | Position (0-based) in the read of the first base in the Spatial Barcode 2 sequence in the given segmented read | +| XM | Z | Segment | Raw Unique Molecular Identifier (UMI) sequence for the given segmented read (for IsoSeq3 compatibility) | +| XC | Z | Segment | Raw Cell Barcode (CBC) sequence for the given segmented read (for IsoSeq3 compatibility) | +| YC | i | Correct | True IFF barcode correction was able to be performed (including "correction" where the original barcode did not change). False otherwise. | +| YP | i | Correct | True IFF the barcode was able to be corrected AND the corrected barcode != the raw barcode. False otherwise. | +| ic | i | Segment | Sum of number of passes from all ZMWs used to create consensus. Always set to 1. (for IsoSeq3 compatibility) | +| im | Z | Segment | ZMW names associated with a given segmented read. Set to the name of the parent read for a segmented read. (e.g. `m64013e_211031_055434/1/ccs`). (for IsoSeq3 compatibility) | +| is | i | Segment | Number of ZMWs associated with a given segmented read. Always set to 1. (for IsoSeq3 compatibility) | +| it | Z | Segment | List of barcodes / UMIs tagged/clipped during segmentation (e.g. `it:Z:CATTAGGTCATCCCTA,AAATTTTGGA`) (for IsoSeq3 compatibility) | +| zm | i | Segment | ZMW number from which the given read originates. (for IsoSeq3 compatibility) | +| XN | Z | Segment, Extract | Altered read name given by Longbow to a segmented read (used for debugging). This name consists of the original read name followed by the start and end positions of the segment on the original read, then the names of the bounding adapters / known regions. For example: `XN:Z:m64013e_211029_235558/24/ccs/0_1960/START-MARS` | +| pz | i | Correct | Offset of the new, corrected, barcode/tag relative to the original, raw value (0-based). NOTE: if the tag could not be corrected, this tag is not present in the output read. | ### Read Tag Types The SAM spec defines the following as types for read tags: diff --git a/src/longbow/inspect/command.py b/src/longbow/inspect/command.py index 721fc8b1..7f01f049 100644 --- a/src/longbow/inspect/command.py +++ b/src/longbow/inspect/command.py @@ -258,7 +258,7 @@ def annotate_read(read, m, max_length, min_rq): fppath = [] if read.has_tag(longbow.utils.constants.SEGMENTS_TAG): - tag = re.split(",", read.get_tag(longbow.utils.constants.SEGMENTS_TAG)) + tag = re.split(longbow.utils.constants.SEGMENT_TAG_DELIMITER, read.get_tag(longbow.utils.constants.SEGMENTS_TAG)) for e in tag: state, rrange = re.split(":", e) diff --git a/src/longbow/pad/command.py b/src/longbow/pad/command.py index 518c6276..563e569c 100644 --- a/src/longbow/pad/command.py +++ b/src/longbow/pad/command.py @@ -258,7 +258,7 @@ def _expand_tag_fn(out_queue, out_bam_header, out_bam_file_name, pbar, res, lb_m # No need to continue here: break - # Write our our read: + # Write out our read: out_bam_file.write(read) # Increment our counters: diff --git a/src/longbow/tagfix/__init__.py b/src/longbow/tagfix/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/src/longbow/tagfix/command.py b/src/longbow/tagfix/command.py new file mode 100644 index 00000000..d04e979a --- /dev/null +++ b/src/longbow/tagfix/command.py @@ -0,0 +1,212 @@ +import logging +import re +import time +import sys +import itertools + +import click +import click_log +import tqdm + +import pysam +import multiprocessing as mp + +from construct import * + +import longbow.utils.constants +from ..utils import bam_utils +from ..utils.cli_utils import format_obnoxious_warning_message + + +PROG_NAME = "tagfix" + +logging.basicConfig(stream=sys.stderr) +logger = logging.getLogger(PROG_NAME) +click_log.basic_config(logger) + + +@click.command(name=logger.name) +@click_log.simple_verbosity_option(logger) +@click.option( + "-t", + "--threads", + type=int, + default=mp.cpu_count() - 1, + show_default=True, + help="number of threads to use (0 for all)", +) +@click.option( + "-o", + "--output-bam", + default="-", + type=click.Path(exists=False), + help="annotated bam output [default: stdout]", +) +@click.option( + '-f', + '--force', + is_flag=True, + default=False, + show_default=True, + help="Force overwrite of the output files if they exist." +) +@click.argument("input-bam", default="-" if not sys.stdin.isatty() else None, type=click.File("rb")) +def main(threads, output_bam, force, input_bam): + """Update longbow read tags after alignment.""" + + t_start = time.time() + + logger.info("Invoked via: longbow %s", " ".join(sys.argv[1:])) + + # Check to see if the output files exist: + bam_utils.check_for_preexisting_files(output_bam, exist_ok=force) + + threads = mp.cpu_count() if threads <= 0 or threads > mp.cpu_count() else threads + logger.info(f"Running with {threads} worker subprocess(es)") + + # Configure process manager: + # NOTE: We're using processes to overcome the Global Interpreter Lock. + manager = mp.Manager() + process_input_data_queue = manager.Queue(threads) + results = manager.Queue() + + pysam.set_verbosity(0) # silence message about the .bai file not being found + with pysam.AlignmentFile( + input_bam, "rb", check_sq=False, require_index=False + ) as bam_file, tqdm.tqdm( + desc="Progress", + unit=" read", + colour="green", + file=sys.stderr, + leave=False, + disable=not sys.stdin.isatty(), + ) as pbar: + + # Start worker sub-processes: + res = manager.dict({"num_tags_corrected": 0, "num_reads": 0}) + worker_process_pool = [] + for _ in range(threads): + p = mp.Process( + target=_correct_read_tags, args=(process_input_data_queue, results, bam_file.header, res) + ) + p.start() + worker_process_pool.append(p) + + # Check if we have run this command on a bam file already: + if bam_utils.bam_header_has_longbow_command_program_group(bam_file.header, PROG_NAME): + logger.error(f"{PROG_NAME} has already been run on input bam: {input_bam}") + sys.exit(1) + + out_header = bam_utils.create_bam_header_with_program_group(logger.name, bam_file.header) + + # Start output worker: + output_worker = mp.Process( + target=_output_writer_fn, + args=( + results, + out_header, + output_bam, + pbar, + ), + ) + output_worker.start() + + # Add in a sentinel value at the end of the queue - one for each subprocess - so we guarantee + # that all subprocesses will exit: + iter_data = itertools.chain(bam_file, (None,) * threads) + for r in iter_data: + if r is not None: + process_input_data_queue.put(r.to_dict()) + else: + process_input_data_queue.put(r) + + # Wait for our input jobs to finish: + for p in worker_process_pool: + p.join() + + # Now that our input processes are done, we can add our exit sentinel onto the output queue and + # wait for that process to end: + results.put(None) + output_worker.join() + + logger.info(f"Corrected tags in {res['num_tags_corrected']} reads of {res['num_reads']} total.") + + et = time.time() + logger.info(f"Done. Elapsed time: {et - t_start:2.2f}s. " + f"Overall processing rate: {res['num_reads']/(et - t_start):2.2f} reads/s.") + + if res['num_tags_corrected'] == 0: + logger.warning(format_obnoxious_warning_message("No read tags were corrected. This is very unlikely. " + "You should check your data.")) + + +def _output_writer_fn(out_queue, out_bam_header, out_bam_file_name, pbar): + """Thread / process fn to write out all our data.""" + + with pysam.AlignmentFile( + out_bam_file_name, "wb", header=out_bam_header + ) as out_bam_file: + while True: + # Wait for some output data: + raw_data = out_queue.get() + + # Check for exit sentinel: + if raw_data is None: + break + + # Unpack data: + read = raw_data + read = pysam.AlignedSegment.from_dict(read, out_bam_header) + + # Write out our read: + out_bam_file.write(read) + + pbar.update(1) + + +def _correct_read_tags(in_queue, out_queue, bam_header, res): + """Function to run in each subprocess. + Do the tag correction here.""" + + while True: + # Wait until we get some data. + # Note: Because we have a sentinel value None inserted at the end of the input data for each + # subprocess, we don't have to add a timeout - we're guaranteed each process will always have + # at least one element. + raw_data = in_queue.get() + + # Check for exit sentinel: + if raw_data is None: + return + + # Unpack our data here: + read = pysam.AlignedSegment.from_dict(raw_data, bam_header) + + if read.is_reverse: + + # Reverse the segments and update the positions: + segments_tag = read.get_tag(longbow.utils.constants.SEGMENTS_TAG) + segments = segments_tag.split(longbow.utils.constants.SEGMENT_TAG_DELIMITER) + read_length = len(read.query_sequence) + new_segments = [] + for seg in reversed(segments): + seg_name, start, end = re.split("[:-]", seg) + new_start = read_length - int(end) + new_end = read_length - int(start) + + new_segments.append(f"{seg_name}:{new_start}-{new_end}") + + read.set_tag(longbow.utils.constants.SEGMENTS_TAG, + longbow.utils.constants.SEGMENT_TAG_DELIMITER.join(new_segments)) + + # Reverse the Segment Qualities: + seg_quals = read.get_tag(longbow.utils.constants.SEGMENTS_QUAL_TAG) + new_seg_quals = seg_quals.split(longbow.utils.constants.SEGMENT_TAG_DELIMITER)[::-1] + read.set_tag(longbow.utils.constants.SEGMENTS_QUAL_TAG, + longbow.utils.constants.SEGMENT_TAG_DELIMITER.join(new_seg_quals)) + + # Increment our counter: + res["num_tags_corrected"] += 1 + + out_queue.put(read.to_dict()) + res["num_reads"] += 1 diff --git a/src/longbow/utils/bam_utils.py b/src/longbow/utils/bam_utils.py index 9ab5e0d6..497cd78e 100644 --- a/src/longbow/utils/bam_utils.py +++ b/src/longbow/utils/bam_utils.py @@ -446,10 +446,25 @@ def get_models_from_bam_header(header): def bam_header_has_model(header): - if 'PG' in header.as_dict(): - for pg in header.as_dict()['PG']: - if pg['PN'] == 'longbow' and 'annotate' in pg['ID']: - return True + try: + if 'PG' in header.as_dict(): + for pg in header.as_dict()['PG']: + if pg['PN'] == 'longbow' and 'annotate' in pg['ID']: + return True + except KeyError: + pass + + return False + + +def bam_header_has_longbow_command_program_group(header, command): + try: + if 'PG' in header.as_dict(): + for pg in header.as_dict()['PG']: + if pg['PN'] == 'longbow' and f"-{command}-" in pg['ID']: + return True + except KeyError: + pass return False diff --git a/src/longbow/utils/constants.py b/src/longbow/utils/constants.py index 4a152325..df2104cd 100644 --- a/src/longbow/utils/constants.py +++ b/src/longbow/utils/constants.py @@ -70,7 +70,7 @@ READ_SPATIAL_BARCODE1_TAG = "X1" READ_SPATIAL_BARCODE1_POS_TAG = "XP" READ_SPATIAL_BARCODE2_TAG = "X2" -READ_SPATIAL_BARCODE2_POS_TAG = "XQ" +READ_SPATIAL_BARCODE2_POS_TAG = "XR" READ_DEMUX_TAG = "id" READ_DEMUX_POS_TAG = "ip" diff --git a/src/longbow/utils/model.py b/src/longbow/utils/model.py index c71eadc8..cd5a20e6 100644 --- a/src/longbow/utils/model.py +++ b/src/longbow/utils/model.py @@ -1338,10 +1338,9 @@ def build_pre_configured_model(model_name): ), "adapters": { "5p_Adapter": "TCTACACGACGCTCTTCCGATCT", - # "Poly_A": "A" * 30, "Poly_A": {HPR_SEGMENT_TYPE_NAME: ("A", 30)}, "3p_Adapter": "GTACTCTGCGTTGATACCACTGCTT", - "SLS": "TTTCTTATATGGG", + "SLS": "TTTCTTATATGGG", # Switch Leader Seq "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", @@ -1540,7 +1539,7 @@ def build_pre_configured_model(model_name): "5p_Adapter": "TCTACACGACGCTCTTCCGATCT", "Poly_A": {HPR_SEGMENT_TYPE_NAME: ("A", 30)}, "3p_Adapter": "CTCTGCGTTGATACCACTGCTT", - "SLS": "TTTCTTATATGGG", + "SLS": "TTTCTTATATGGG", # Switch Leader Seq "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", @@ -1634,7 +1633,7 @@ def build_pre_configured_model(model_name): "5p_Adapter": "TCTACACGACGCTCTTCCGATCT", "Poly_A": {HPR_SEGMENT_TYPE_NAME: ("A", 30)}, "3p_Adapter": "GTACTCTGCGTTGATACCACTGCTT", - "SLS": "TTTCTTATATGGG", + "SLS": "TTTCTTATATGGG", # Switch Leader Seq "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", "D": "ACCTCCTCCTCCAGAA", @@ -1703,7 +1702,7 @@ def build_pre_configured_model(model_name): # V V # Spatial Barcode 2 Spatial Barcode 1 "description": "The Slide-seq 15 array element model.", - "version": "2.0.1", + "version": "2.0.2", "array_element_structure": ( ("A", "5p_Adapter", "SBC2", "SLS2", "SBC1", "UMI", "Poly_T", "cDNA", "3p_Adapter"), ("B", "5p_Adapter", "SBC2", "SLS2", "SBC1", "UMI", "Poly_T", "cDNA", "3p_Adapter"), @@ -1724,7 +1723,7 @@ def build_pre_configured_model(model_name): "adapters": { "5p_Adapter": "TCTACACGACGCTCTTCCGATCT", "3p_Adapter": "CCCATGTACTCTGCGTTGATACCACTGCTT", - "SLS2": "TCTTCAGCGTTCCCGAGA", + "SLS2": "TCTTCAGCGTTCCCGAGA", # Switch Leader Seq "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", diff --git a/tests/integration/test_tagfix.py b/tests/integration/test_tagfix.py new file mode 100644 index 00000000..b05330b5 --- /dev/null +++ b/tests/integration/test_tagfix.py @@ -0,0 +1,80 @@ +import pytest +import os +import sys +import subprocess + +from click.testing import CliRunner + +from longbow.__main__ import main_entry as longbow + +from ..utils import assert_reads_files_equal +from ..utils import cat_file_to_pipe +from ..utils import convert_sam_to_bam + +################################################################################ + +TOOL_NAME = "tagfix" + +TEST_DATA_FOLDER = path = os.path.abspath( + __file__ + os.path.sep + "../../" + os.path.sep + "test_data" +) + os.path.sep + TOOL_NAME + os.path.sep + + +################################################################################ + + +@pytest.mark.parametrize("input_sam, expected_sam", [ + [ + TEST_DATA_FOLDER + "tagfix_test_data.sam", + TEST_DATA_FOLDER + "tagfix_test_data.expected.sam" + ], +]) +def test_tagfix(tmpdir, input_sam, expected_sam): + + # Convert test files to bam: + input_bam = tmpdir.join("input.bam") + convert_sam_to_bam(input_sam, input_bam) + + expected_bam = tmpdir.join("expected.bam") + convert_sam_to_bam(expected_sam, expected_bam) + + actual_bam_out = tmpdir.join(f"{TOOL_NAME}_actual_out.bam") + args = ["tagfix", "-t", 1, "-v", "INFO", "-o", str(actual_bam_out), str(input_bam)] + + runner = CliRunner(mix_stderr=False) + result = runner.invoke(longbow, args) + assert result.exit_code == 0 + + # Equal files result as True: + assert_reads_files_equal(actual_bam_out, expected_bam, order_matters=True) + + +@pytest.mark.skip(reason="tagfix pipe input test is not working properly and needs to be debugged.") +@pytest.mark.parametrize("input_sam, expected_sam", [ + [ + TEST_DATA_FOLDER + "tagfix_test_data.sam", + TEST_DATA_FOLDER + "tagfix_test_data.expected.sam" + ], +]) +def test_tagfix_from_pipe(tmpdir, input_sam, expected_sam): + + # Convert test files to bam: + input_bam = tmpdir.join("input.bam") + convert_sam_to_bam(input_sam, input_bam) + + expected_bam = tmpdir.join("expected.bam") + convert_sam_to_bam(expected_sam, expected_bam) + + actual_bam_out = tmpdir.join(f"{TOOL_NAME}_actual_out.bam") + + proc = subprocess.Popen( + [sys.executable, "-m", "longbow", "tagfix", "-t", 1, "-v", "INFO", "-o", str(actual_bam_out)], + stdin=subprocess.PIPE + ) + + cat_file_to_pipe(str(input_bam), proc) + + assert proc.returncode == 0 + + # Equal files result as True: + assert_reads_files_equal(actual_bam_out, expected_bam, order_matters=True) diff --git a/tests/test_data/models/mas_15_spatial_slide-seq_single_none.json b/tests/test_data/models/mas_15_spatial_slide-seq_single_none.json index a421b160..e60db33c 100644 --- a/tests/test_data/models/mas_15_spatial_slide-seq_single_none.json +++ b/tests/test_data/models/mas_15_spatial_slide-seq_single_none.json @@ -1,7 +1,7 @@ { "name": "mas_15_spatial_slide-seq_single_none", "description": "The Slide-seq 15 array element model.", - "version": "2.0.1", + "version": "2.0.2", "array_element_structure": [ [ "A", @@ -328,4 +328,4 @@ ] ] } -} \ No newline at end of file +} diff --git a/tests/test_data/tagfix/tagfix_test_data.expected.sam b/tests/test_data/tagfix/tagfix_test_data.expected.sam new file mode 100644 index 00000000..c9716841 --- /dev/null +++ b/tests/test_data/tagfix/tagfix_test_data.expected.sam @@ -0,0 +1,224 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 +@SQ SN:chr2 LN:242193529 +@SQ SN:chr3 LN:198295559 +@SQ SN:chr4 LN:190214555 +@SQ SN:chr5 LN:181538259 +@SQ SN:chr6 LN:170805979 +@SQ SN:chr7 LN:159345973 +@SQ SN:chr8 LN:145138636 +@SQ SN:chr9 LN:138394717 +@SQ SN:chr10 LN:133797422 +@SQ SN:chr11 LN:135086622 +@SQ SN:chr12 LN:133275309 +@SQ SN:chr13 LN:114364328 +@SQ SN:chr14 LN:107043718 +@SQ SN:chr15 LN:101991189 +@SQ SN:chr16 LN:90338345 +@SQ SN:chr17 LN:83257441 +@SQ SN:chr18 LN:80373285 +@SQ SN:chr19 LN:58617616 +@SQ SN:chr20 LN:64444167 +@SQ SN:chr21 LN:46709983 +@SQ SN:chr22 LN:50818468 +@SQ SN:chrX LN:156040895 +@SQ SN:chrY LN:57227415 +@SQ SN:chrM LN:16569 +@SQ SN:chr1_KI270706v1_random LN:175055 +@SQ SN:chr1_KI270707v1_random LN:32032 +@SQ SN:chr1_KI270708v1_random LN:127682 +@SQ SN:chr1_KI270709v1_random LN:66860 +@SQ SN:chr1_KI270710v1_random LN:40176 +@SQ SN:chr1_KI270711v1_random LN:42210 +@SQ SN:chr1_KI270712v1_random LN:176043 +@SQ SN:chr1_KI270713v1_random LN:40745 +@SQ SN:chr1_KI270714v1_random LN:41717 +@SQ SN:chr2_KI270715v1_random LN:161471 +@SQ SN:chr2_KI270716v1_random LN:153799 +@SQ SN:chr3_GL000221v1_random LN:155397 +@SQ SN:chr4_GL000008v2_random LN:209709 +@SQ SN:chr5_GL000208v1_random LN:92689 +@SQ SN:chr9_KI270717v1_random LN:40062 +@SQ SN:chr9_KI270718v1_random LN:38054 +@SQ SN:chr9_KI270719v1_random LN:176845 +@SQ SN:chr9_KI270720v1_random LN:39050 +@SQ SN:chr11_KI270721v1_random LN:100316 +@SQ SN:chr14_GL000009v2_random LN:201709 +@SQ SN:chr14_GL000225v1_random LN:211173 +@SQ SN:chr14_KI270722v1_random LN:194050 +@SQ SN:chr14_GL000194v1_random LN:191469 +@SQ SN:chr14_KI270723v1_random LN:38115 +@SQ SN:chr14_KI270724v1_random LN:39555 +@SQ SN:chr14_KI270725v1_random LN:172810 +@SQ SN:chr14_KI270726v1_random LN:43739 +@SQ SN:chr15_KI270727v1_random LN:448248 +@SQ SN:chr16_KI270728v1_random LN:1872759 +@SQ SN:chr17_GL000205v2_random LN:185591 +@SQ SN:chr17_KI270729v1_random LN:280839 +@SQ SN:chr17_KI270730v1_random LN:112551 +@SQ SN:chr22_KI270731v1_random LN:150754 +@SQ SN:chr22_KI270732v1_random LN:41543 +@SQ SN:chr22_KI270733v1_random LN:179772 +@SQ SN:chr22_KI270734v1_random LN:165050 +@SQ SN:chr22_KI270735v1_random LN:42811 +@SQ SN:chr22_KI270736v1_random LN:181920 +@SQ SN:chr22_KI270737v1_random LN:103838 +@SQ SN:chr22_KI270738v1_random LN:99375 +@SQ SN:chr22_KI270739v1_random LN:73985 +@SQ SN:chrY_KI270740v1_random LN:37240 +@SQ SN:chrUn_KI270302v1 LN:2274 +@SQ SN:chrUn_KI270304v1 LN:2165 +@SQ SN:chrUn_KI270303v1 LN:1942 +@SQ SN:chrUn_KI270305v1 LN:1472 +@SQ SN:chrUn_KI270322v1 LN:21476 +@SQ SN:chrUn_KI270320v1 LN:4416 +@SQ SN:chrUn_KI270310v1 LN:1201 +@SQ SN:chrUn_KI270316v1 LN:1444 +@SQ SN:chrUn_KI270315v1 LN:2276 +@SQ SN:chrUn_KI270312v1 LN:998 +@SQ SN:chrUn_KI270311v1 LN:12399 +@SQ SN:chrUn_KI270317v1 LN:37690 +@SQ SN:chrUn_KI270412v1 LN:1179 +@SQ SN:chrUn_KI270411v1 LN:2646 +@SQ SN:chrUn_KI270414v1 LN:2489 +@SQ SN:chrUn_KI270419v1 LN:1029 +@SQ SN:chrUn_KI270418v1 LN:2145 +@SQ SN:chrUn_KI270420v1 LN:2321 +@SQ SN:chrUn_KI270424v1 LN:2140 +@SQ SN:chrUn_KI270417v1 LN:2043 +@SQ SN:chrUn_KI270422v1 LN:1445 +@SQ SN:chrUn_KI270423v1 LN:981 +@SQ SN:chrUn_KI270425v1 LN:1884 +@SQ SN:chrUn_KI270429v1 LN:1361 +@SQ SN:chrUn_KI270442v1 LN:392061 +@SQ SN:chrUn_KI270466v1 LN:1233 +@SQ SN:chrUn_KI270465v1 LN:1774 +@SQ SN:chrUn_KI270467v1 LN:3920 +@SQ SN:chrUn_KI270435v1 LN:92983 +@SQ SN:chrUn_KI270438v1 LN:112505 +@SQ SN:chrUn_KI270468v1 LN:4055 +@SQ SN:chrUn_KI270510v1 LN:2415 +@SQ SN:chrUn_KI270509v1 LN:2318 +@SQ SN:chrUn_KI270518v1 LN:2186 +@SQ SN:chrUn_KI270508v1 LN:1951 +@SQ SN:chrUn_KI270516v1 LN:1300 +@SQ SN:chrUn_KI270512v1 LN:22689 +@SQ SN:chrUn_KI270519v1 LN:138126 +@SQ SN:chrUn_KI270522v1 LN:5674 +@SQ SN:chrUn_KI270511v1 LN:8127 +@SQ SN:chrUn_KI270515v1 LN:6361 +@SQ SN:chrUn_KI270507v1 LN:5353 +@SQ SN:chrUn_KI270517v1 LN:3253 +@SQ SN:chrUn_KI270529v1 LN:1899 +@SQ SN:chrUn_KI270528v1 LN:2983 +@SQ SN:chrUn_KI270530v1 LN:2168 +@SQ SN:chrUn_KI270539v1 LN:993 +@SQ SN:chrUn_KI270538v1 LN:91309 +@SQ SN:chrUn_KI270544v1 LN:1202 +@SQ SN:chrUn_KI270548v1 LN:1599 +@SQ SN:chrUn_KI270583v1 LN:1400 +@SQ SN:chrUn_KI270587v1 LN:2969 +@SQ SN:chrUn_KI270580v1 LN:1553 +@SQ SN:chrUn_KI270581v1 LN:7046 +@SQ SN:chrUn_KI270579v1 LN:31033 +@SQ SN:chrUn_KI270589v1 LN:44474 +@SQ SN:chrUn_KI270590v1 LN:4685 +@SQ SN:chrUn_KI270584v1 LN:4513 +@SQ SN:chrUn_KI270582v1 LN:6504 +@SQ SN:chrUn_KI270588v1 LN:6158 +@SQ SN:chrUn_KI270593v1 LN:3041 +@SQ SN:chrUn_KI270591v1 LN:5796 +@SQ SN:chrUn_KI270330v1 LN:1652 +@SQ SN:chrUn_KI270329v1 LN:1040 +@SQ SN:chrUn_KI270334v1 LN:1368 +@SQ SN:chrUn_KI270333v1 LN:2699 +@SQ SN:chrUn_KI270335v1 LN:1048 +@SQ SN:chrUn_KI270338v1 LN:1428 +@SQ SN:chrUn_KI270340v1 LN:1428 +@SQ SN:chrUn_KI270336v1 LN:1026 +@SQ SN:chrUn_KI270337v1 LN:1121 +@SQ SN:chrUn_KI270363v1 LN:1803 +@SQ SN:chrUn_KI270364v1 LN:2855 +@SQ SN:chrUn_KI270362v1 LN:3530 +@SQ SN:chrUn_KI270366v1 LN:8320 +@SQ SN:chrUn_KI270378v1 LN:1048 +@SQ SN:chrUn_KI270379v1 LN:1045 +@SQ SN:chrUn_KI270389v1 LN:1298 +@SQ SN:chrUn_KI270390v1 LN:2387 +@SQ SN:chrUn_KI270387v1 LN:1537 +@SQ SN:chrUn_KI270395v1 LN:1143 +@SQ SN:chrUn_KI270396v1 LN:1880 +@SQ SN:chrUn_KI270388v1 LN:1216 +@SQ SN:chrUn_KI270394v1 LN:970 +@SQ SN:chrUn_KI270386v1 LN:1788 +@SQ SN:chrUn_KI270391v1 LN:1484 +@SQ SN:chrUn_KI270383v1 LN:1750 +@SQ SN:chrUn_KI270393v1 LN:1308 +@SQ SN:chrUn_KI270384v1 LN:1658 +@SQ SN:chrUn_KI270392v1 LN:971 +@SQ SN:chrUn_KI270381v1 LN:1930 +@SQ SN:chrUn_KI270385v1 LN:990 +@SQ SN:chrUn_KI270382v1 LN:4215 +@SQ SN:chrUn_KI270376v1 LN:1136 +@SQ SN:chrUn_KI270374v1 LN:2656 +@SQ SN:chrUn_KI270372v1 LN:1650 +@SQ SN:chrUn_KI270373v1 LN:1451 +@SQ SN:chrUn_KI270375v1 LN:2378 +@SQ SN:chrUn_KI270371v1 LN:2805 +@SQ SN:chrUn_KI270448v1 LN:7992 +@SQ SN:chrUn_KI270521v1 LN:7642 +@SQ SN:chrUn_GL000195v1 LN:182896 +@SQ SN:chrUn_GL000219v1 LN:179198 +@SQ SN:chrUn_GL000220v1 LN:161802 +@SQ SN:chrUn_GL000224v1 LN:179693 +@SQ SN:chrUn_KI270741v1 LN:157432 +@SQ SN:chrUn_GL000226v1 LN:15008 +@SQ SN:chrUn_GL000213v1 LN:164239 +@SQ SN:chrUn_KI270743v1 LN:210658 +@SQ SN:chrUn_KI270744v1 LN:168472 +@SQ SN:chrUn_KI270745v1 LN:41891 +@SQ SN:chrUn_KI270746v1 LN:66486 +@SQ SN:chrUn_KI270747v1 LN:198735 +@SQ SN:chrUn_KI270748v1 LN:93321 +@SQ SN:chrUn_KI270749v1 LN:158759 +@SQ SN:chrUn_KI270750v1 LN:148850 +@SQ SN:chrUn_KI270751v1 LN:150742 +@SQ SN:chrUn_KI270752v1 LN:27745 +@SQ SN:chrUn_KI270753v1 LN:62944 +@SQ SN:chrUn_KI270754v1 LN:40191 +@SQ SN:chrUn_KI270755v1 LN:36723 +@SQ SN:chrUn_KI270756v1 LN:79590 +@SQ SN:chrUn_KI270757v1 LN:71251 +@SQ SN:chrUn_GL000214v1 LN:137718 +@SQ SN:chrUn_KI270742v1 LN:186739 +@SQ SN:chrUn_GL000216v2 LN:176608 +@SQ SN:chrUn_GL000218v1 LN:161147 +@SQ SN:chrEBV LN:171823 +@PG PN:minimap2 ID:minimap2 VN:2.24-r1122 CL:minimap2 -ayYL --MD --eqx -x splice:hq -t 4 /cromwell_root/broad-dsde-methods-long-reads/resources/references/grch38_noalt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa tmp.fastq +@PG PN:restore-annotations ID:restore-annotations-0.0.1 VN:0.0.1 DS:Reads an unaligned bam with annotations and an aligned bam containing the same reads. Copies tags on the unaligned bam to reads in the aligned file with the same name. CL:/lrma/restore_annotations_to_aligned_bam.py --bam shard.bam --aligned-bam out.bam --out-name out.AnnotationsRestored.bam +@PG ID:GATK PrintReads VN:4.2.4.1-1-gcaa48f9 CL:PrintReads --output out.bam --input aligned.bam --read-filter MappedReadFilter --read-filter MappingQualityNotZeroReadFilter --read-filter NotSecondaryAlignmentReadFilter --read-filter NotSupplementaryAlignmentReadFilter --read-filter ReadLengthReadFilter --read-filter ExcessiveEndClippedReadFilter --disable-read-filter WellformedReadFilter --max-read-length 15000 --max-clipped-bases 1000 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --min-read-length 1 PN:GATK PrintReads +@PG PN:longbow ID:longbow-pad-0.5.27 VN:0.5.27 DS:Pad tag by specified number of adjacent bases from the read. MODEL(s): {"name": "mas15v2", "description": "The standard MAS-seq 15 array element model.", "version": "2.0.0", "array_element_structure": [["A", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["B", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["C", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["D", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["E", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["F", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["G", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["H", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["I", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["J", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["K", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["L", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["M", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["N", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["O", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS", "P"]], "adapters": {"VENUS": "TCTACACGACGCTCTTCCGATCT", "Poly_A": {"HomopolymerRepeat": ["A", 30]}, "MARS": "GTACTCTGCGTTGATACCACTGCTT", "BOREAS": "TTTCTTATATGGG", "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", "D": "ACCTCCTCCTCCAGAA", "E": "AACCGGACACACTTAG", "F": "AGAGTCCAATTCGCAG", "G": "AATCAAGGCTTAACGG", "H": "ATGTTGAATCCTAGCG", "I": "AGTGCGTTGCGAATTG", "J": "AATTGCGTAGTTGGCC", "K": "ACACTTGGTCGCAATC", "L": "AGTAAGCCTTCGTGTC", "M": "ACCTAGATCAGAGCCT", "N": "AGGTATGCCGGTTAAG", "O": "AAGTCACCGGCACCTT", "P": "ATGAAGTGGCTCGAGA", "CBC": {"FixedLengthRandomBases": 16}, "UMI": {"FixedLengthRandomBases": 10}, "cDNA": "random"}, "direct_connections": {"Poly_A": ["MARS"], "MARS": ["K", "P", "D", "G", "J", "E", "A", "F", "N", "O", "M", "C", "H", "I", "B", "L"], "A": ["VENUS"], "B": ["VENUS"], "C": ["VENUS"], "D": ["VENUS"], "E": ["VENUS"], "F": ["VENUS"], "G": ["VENUS"], "H": ["VENUS"], "I": ["VENUS"], "J": ["VENUS"], "K": ["VENUS"], "L": ["VENUS"], "M": ["VENUS"], "N": ["VENUS"], "O": ["VENUS"], "P": ["VENUS"], "VENUS": ["CBC"], "CBC": ["UMI"], "UMI": ["BOREAS"], "BOREAS": ["cDNA"], "cDNA": ["Poly_A"]}, "start_element_names": ["A", "VENUS"], "end_element_names": ["P", "Poly_A"], "named_random_segments": ["UMI", "CBC", "cDNA"], "coding_region": "cDNA", "annotation_segments": {"UMI": [["ZU", "XU"], ["XM", "XU"]], "CBC": [["CR", "XB"], ["XC", "XB"]]}} CL:/longbow/venv/bin/longbow pad --model mas15v2 -v INFO --barcode-tag CR -e 2 -o tmp.bam -n CR shard_0.bam +@PG PN:longbow ID:longbow-correct-0.5.28 VN:0.5.28 DS:Correct tag to values provided in barcode allowlist. MODEL(s): {"name": "mas15v2", "description": "The standard MAS-seq 15 array element model.", "version": "2.0.0", "array_element_structure": [["A", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["B", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["C", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["D", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["E", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["F", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["G", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["H", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["I", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["J", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["K", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["L", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["M", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["N", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["O", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS", "P"]], "adapters": {"VENUS": "TCTACACGACGCTCTTCCGATCT", "Poly_A": {"HomopolymerRepeat": ["A", 30]}, "MARS": "GTACTCTGCGTTGATACCACTGCTT", "BOREAS": "TTTCTTATATGGG", "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", "D": "ACCTCCTCCTCCAGAA", "E": "AACCGGACACACTTAG", "F": "AGAGTCCAATTCGCAG", "G": "AATCAAGGCTTAACGG", "H": "ATGTTGAATCCTAGCG", "I": "AGTGCGTTGCGAATTG", "J": "AATTGCGTAGTTGGCC", "K": "ACACTTGGTCGCAATC", "L": "AGTAAGCCTTCGTGTC", "M": "ACCTAGATCAGAGCCT", "N": "AGGTATGCCGGTTAAG", "O": "AAGTCACCGGCACCTT", "P": "ATGAAGTGGCTCGAGA", "CBC": {"FixedLengthRandomBases": 16}, "UMI": {"FixedLengthRandomBases": 10}, "cDNA": "random"}, "direct_connections": {"Poly_A": ["MARS"], "MARS": ["J", "N", "A", "F", "G", "H", "L", "O", "B", "P", "I", "E", "K", "C", "M", "D"], "A": ["VENUS"], "B": ["VENUS"], "C": ["VENUS"], "D": ["VENUS"], "E": ["VENUS"], "F": ["VENUS"], "G": ["VENUS"], "H": ["VENUS"], "I": ["VENUS"], "J": ["VENUS"], "K": ["VENUS"], "L": ["VENUS"], "M": ["VENUS"], "N": ["VENUS"], "O": ["VENUS"], "P": ["VENUS"], "VENUS": ["CBC"], "CBC": ["UMI"], "UMI": ["BOREAS"], "BOREAS": ["cDNA"], "cDNA": ["Poly_A"]}, "start_element_names": ["VENUS", "A"], "end_element_names": ["Poly_A", "P"], "named_random_segments": ["CBC", "cDNA", "UMI"], "coding_region": "cDNA", "annotation_segments": {"UMI": [["ZU", "XU"], ["XM", "XU"]], "CBC": [["CR", "XB"], ["XC", "XB"]]}} CL:/longbow/venv/bin/longbow correct -t 1 --model mas15v2 --allow-list short_read_barcodes_no_counts.txt -v INFO --barcode-tag CR --corrected-tag CB --max-hifi-dist 2 --max-clr-dist 2 -o shard_0_corrected_barcodes.bam --barcode-uncorrectable-bam shard_0_uncorrected_barcodes.bam shard_0.bam +@PG PN:samtools ID:samtools VN:1.11 PP:longbow-correct-0.5.28 CL:samtools view -hb tests/test_data/tagfix/tagfix_test_data.sam +@PG PN:longbow ID:longbow-tagfix-0.5.32 VN:0.5.32 DS:Update longbow read tags after alignment. CL:/Users/jonn/Development/longbow_main/venv/bin/longbow tagfix -t1 -f tagfix_test.bam -o tagfix_test.OUT.bam +@PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools view -h tagfix_test.OUT.bam +read_rev_1 16 chr1 14362 5 120S102=1X365=140N69=757N24=1X70=78S * 0 0 ATCTCGAGCCACTTCATAAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACTGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTTCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACCCCATATAAGAAAGCCCTTCAGTATCTTGGGACCGGTGTAGATCGGAAGAGCGTCGTGTAGAAAGGTGCCGGTGACTT ~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+~~~~~~~~~~~~~~~~~~~~~j~~~~~~S~~~~~~~~~~~x~~{~~~~~~~~~r~~~U~~~~~~~~r~x~~~w~~~~dh~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~p~~~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~J~~~~S~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~~~~~~t~~j~~~m~~~~~~~~~~y~~~~~~~~|~~~~~~~~x~~~~~~~~x~x~~~~~~~I~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~W~~~~~w~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~p~~~s~~~~~~~~~~~~~~l~~~}~~~~~~~~|~~x~~~{~~~~~~~~~~k~~~~~~~~x~~w~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~j~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~y~p~~~~~~~~~~~~ SG:Z:P:1-17,MARS:18-42,Poly_A:43-121,cDNA:122-751,BOREAS:752-765,UMI:766-775,CBC:776-791,VENUS:792-814,O:815-830 XQ:Z:32/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,44/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,52/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,52/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,54/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,50/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,42/46 +read_rev_2 16 chr1 14366 40 173S6=1I13=1I16=1I21=1X6=1I3=1D4=1D12=1D3=1X9=1X23=2D7=1D29=2X3=1I16=1D7=1X5=1I16=1I8=2I14=1D23=1D9=1D8=1D15=1I8=2X18=1I19=1X2=1X8=1D9=1D7=1I6=1I38=1D13=1X8=1I10=1I5=1X10=1D140N11=1X12=1X3=2I5=1I5=1I5=1I23=1D5=1I35=1X13=2X3=1X18=1X5=1D5=1I58=1X14=1D12=1D6=1X1=1I11=1D25=77S * 0 0 AAGCAGTGTATCAACGCAGAAGTACTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTGTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTATTTTTTTTATTTTTTTTATTTTTTTATTATTTTATTTTTTTTCCGCACAGTCTAGAGATCCTTTAATTAAAAGCACACTGTATGGTTTCTGCTCAGTTCTTTAATGATTGTGTGGCCGTTTCTCTGGAAGCTCATAAGAACACTGTGGCGCAGGCTGGGTGGAGCCGCCCCCATGAGCACAGGCAGACAGAAGTCCCCGCCCCCACTGTTGTGGCCTCAAGCCAGCTTCCGCACCTTGAAAGCTGGTCTCCACACAAGTGCTGGTTTTCCGTCACCCCCTCCAAGGAAGTAGGTCTGAGCAGCTGTCCTGGCGTGTCCATTCAGAGCAACGGCCCGAAGTCTGGTCCTGGGGGGGAAGGTGTCATTGGAGCCCCCTACGATTCCAAGACGTCCTCGCCTCCTCTGCTGTGGCATGCTGCGGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAGGCTCCTCCGGACCCCTCACACAGCCCCAGGTTCCTTACCCAGAGATGCCTTGCGCCTCGTGACCAGCTTGTAGAAGTGAGATCCCGACAATCAACGTGCCCACCTTGGCTCGTGGCTCCACTGCCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCATTCACATGCGACCGTGGACACCCTGTCCCCACCCCCATTACACTCCCAGACCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAACACCGGGCACTGATAGACAGCGGCTGTTGAGGCGCCCACCTCCCAGCACCTCGGGGCCAGGGCCAGGGTGTCCCCAAATAAGAAACACGCGGCTTGCTTGGTGAATGTAGAGACCGAAGAGCGTCCGTGTAGAGCCAACTACGCACTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SG:Z:MARS:1-25,Poly_A:26-171,cDNA:172-929,BOREAS:930-943,UMI:944-953,CBC:954-969,VENUS:970-991,J:992-1006 XQ:Z:0/0,23/26,0/0,0/0,38/46,26/32,43/50,46/60,0/0,26/26,0/0,0/0,42/46,25/32,40/50,60/60,0/0,22/26,0/0,0/0,31/46,24/32,38/50,50/60,0/0,26/26,0/0,0/0,34/46,27/32,42/50,30/60,0/0,22/26,0/0,0/0,37/46,30/32,38/50,54/60,0/0,26/26,0/0,0/0,42/46,22/32,43/50,56/60,0/0,26/26,0/0,0/0,40/46,24/32,43/50,50/60,0/0,21/26,0/0,0/0,41/46,30/32,38/50,52/60,0/0,26/26,0/0,0/0,42/46,20/32,42/50,55/60,0/0,26/26,0/0,0/0,44/46,32/32,38/50,52/60,0/0,24/26,0/0,0/0,43/46,27/32,35/50,54/60,0/0,26/26,0/0,0/0,38/46,22/32 +read_rev_3 16 chr1 14368 41 80S14=1I4=1I16=1I7=2I1X11=2X2=2X5=2I14=2I29=1I1=3I11=1X2=7I17=1D24=1I4=1X4=1I5=1I3=2I9=1I3=1D12=2X11=1X5=1I8=1I1=1I2=1X3=2I6=1I8=3I1=1I7=1D11=1X28=5I3=4I8=1I3=1D1=1D4=1D14=1I9=1X2=1I16=1I5=1I2=2I5=1D3=1I3=1I3=8I7=3I2=2I11=4I6=1X12=1X2=2I2=1I3=1X7=1I1=1I17=140N5=1I37=1I17=1I10=757N3=2I3=1D7=1X1=1X3=1D1=1D1=1X1=1D7=1I3=4I2=1D2=1D15=1I6=2X6=1I13=1I11=1D1X2=1D1=1X2=1I3=2I1=1I5=2X5=2I2=3I4=1X12=1I12=659N7=3I10=1I6=1I4=1D1=1X5=7I7=2X3=1D9=1X3=2I5=1X7=15I1=1I7=6I15=1I6=1D6=1I4=1I1=2I1=2I9=18I5=1I8=11I2=1X1=1D1=1X9=1I2=1X1=1X92N9=1I9=1I15=2I8=1X3=2X4=2I13=5I4=1I7=8I3=4I18=1I5=1I2=1I10=2I3=1I1X8=1I5=1D32=1I11=2X1=1X20=177N3=1X2=1I10=1I5=2I5=2D4=1I9=1D12=1X9=1I2=1I7=1D3=2I5=1X7=1X2=2I1=1I2=1I8=1I2=1X8=1I3=1I3=6I7=2I3=1X4=237N1X7=1D4=1I4=1X15=1I2=2I3=1D4=2I17=1D3=1X7=1X6=2X17=1I4=7I3=1I6=1X2=3X4=1X1=1I7=2X5=172N15=1I1X1=3I8=1X3=1I2=1I9=1X9=3I5=4I7=1I10=2I10=1I4=1I9=21I4=1X6=1X16=1X1=5I4=1D2=1D10=2I1=1D2=206N6=1D5=2I1=1X13=1D7=3I1X35=1I2=1I6=1X2=1I8=332S * 0 0 AAGCGAGTGGTGTATCAACGCAGAGTACATTTTTTTTTTTTTTTCTTTTTTTATTTTTTTTTTGTTTTTTTACTTGCACTACAGCTAGAGATCCTTTTATTTAAAAGCACACTGTTGGGTTTCTCCCCTCAGTTCTTTTATGCATGGTGTTTGCCGTTTTCTCTGGAGAAGCCTCTTAAGAACACAGTGGCGCAGGACTTGTGGGTGGAGCCTTCCATCCCACCCCCATGGAGCACAGGAGACAGAAGTCCCCGCCCCAGCTGATGTGACCTCAAAGCCTAGCCTCTTCCGCTCACTTAAGCTGGTCTCCCAACAGTGCTGGTACCGTCAACCCCCTCACACATGGACCAGTAGGTTCTGAGCACACGTCTTGTCCGGCTGTGTCCAGGTCAGAGCAACGGCCCAAGTCTGGGTCTTGGGCGGGACATGGGGAAGGTTGTAGGAGCCCCTACGATTCCCTAGTCGTCCTTGTCCCTCCTCTGCCTGTGGCCTGCTGGCGTGGTGGGGCAAGACGGACGGTGGTTGGGATGGATAAGTCTCTGACACGCGGTCTGGCAAAAGCTCCTCCGGGCACCTATCTACCCGCCCCAGTGTTCCTTTCCCAGAGATGCCCTTGCCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCATAGTGCCCACCTTGGCTCTGTGGCTCTCACTTTGGCTCTGCTCCGTATGCGTTCTCTCCAGTCTTCTAGTCCTCTTCATGCTGCGCAGCCTTGGCTGTGCCGATTGCCCCCAGCTTGAGCGGATGGACTGAGAAAGTTGGACCACAGCCCTCGGAGGCGGATTGTCATCCACTTCCCTGGTGAGCTCCCTGGACTGAAGGGGTAGACGCGCTGCCTGCTGACTGTGGCCTGCCTGGCATCTGGCGCACTGGCTACAGGGGACGCTAGGTTGTGGGTGGGCGACGCTGTAGGAGCATGTGGGGGGTCTGTTGCACTGGCCAGCACACTCAGGGCTGGGCGGTGTGATTCCGGTGGGGGCGTCGGTACGGTCTGGGGTGGTGGTGGGTGGTGCGAGGGTGGTTTTTGAACCCATCTTGTTATGGCTTGAGAGGCCTCGGCTACACTCAGTGTGGAAGGTGGGGGCAGTTATGGTTTGGTTGGCCAGGGGCAGAGGCCGTGGGGCCAATGCCGTGGCAGGGGGCCCAGCCCAGGTCGGCAATGTACCATGACGGTTCGTTGGCAACTTGCAAGGGCAGGTACAGGCGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCCAGGTCTGGACCTTAGAAGTAGTTCTCTGGGACCTGTTGTTTCCAGCTGCTTCTCTGGCTTGCATGGAACAAGGGGGATCAAACAGCTTATCCTCTGTCTTCTTGCCCCCGCAACTCACAGGGGTCTTAGTAATGACAAGCACCAGCCCTGGGGGTCCAAGGAAAGAAAAAAACATACTTATCTCCTACTGGTTCTCGTGGTTGTTCAAGAGCAGCAAGGAGTCTAGGACGAGCCTTGATGTTGCTGGGAAGACCCAAAGTCCCGCTTCTGATTCGTCCTCGGGCTCCGGTCTTGCAAGTGCGTGCCTCACGAACCTCGGAATGCTCCTTCAAGTTCTCCTGCAGGGCCCGCTCAATACACCAGGGGGAGGTCGCTTTGCTCTGGGTCCTGTGGCCTAGGGGGCATCCGTCTCTCGCAGGCCAGGGCGTCCTGGGCGCCCCGTTGAAGATGGAAATACGAAGAATGAAATGGTAGCCTTATTCCAGCAGGCGCCCTGGAGCTGCGGGAGGTATTGCACTGGAGATTAACCTTGATGCCTTTCCGTGCTGCCCTTGATTTCTCAACCCCCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGACCGTGCACCGGGCCTCCGGCTTATCGCCTCTAACATGCTGAAGATGTCTGCAGGACCCTTCTATGCAGTACTGCAGGGCATTTTTCCGCCATCTGTGGTGGCCTACCTCTCGCGCAGGTCTGGACACCACCCCTGGATGAGGGGCTAGGCATAGGTCTGTACCTGCAAGGGGCTCATAGAGCTGCATCTACTACACAGGGAGTCATGGAGCCCCCCCCCCCCCCCCGGCTGCGGCCGCCTACCGGAAAGCTCCCCGCCGCACCCCATATATAGAAAATAGGGTGGGATCGACCGATGGTCTATAGATCGGAAATAATGAAGGAGCGGCGCTGTAGACGCTAGGATTCAACAAT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SG:Z:MARS:1-28,Poly_A:29-71,cDNA:72-2137,BOREAS:2138-2152,UMI:2153-2162,CBC:2163-2178,VENUS:2179-2212,H:2213-2229 XQ:Z:0/0,17/26,0/0,0/0,38/46,30/32,35/50,60/60,0/0,15/26,0/0,0/0,46/46,25/32,29/50,56/60,0/0,23/26,0/0,0/0,25/46,27/32,41/50,54/60,0/0,23/26,0/0,0/0,28/46,28/32,36/50,51/60,0/0,8/26,0/0 +read_rev_4 16 chr1 14398 1 50S5=1X2=1I16=1D1X12=1D1X18=5I4=1X3=1D20=1I6=1X25=1I12=1I3=1I1X9=1X2=2X4=2X5=1I13=3I3=1X9=1I13=1I2=2X3=1X5=1X5=2I1=1I1X5=1I12=1D3=1D13=1X5=3I13=1X9=1I1=1I4=1D18=1I2=1D12=1I2=1I12=2X20=1I11=1X14=1D8=1D10=2I2=1D7=1I4=2I1=1I4=2I5=1X2=140N2=1D5=4I6=1D5=1I13=1D7=1I4=1X23=171278N1=1X1=1D2=1I17=1X8=1I11=2I2=1I3=1X4=1I6=1X1=1X21=1I1X11=13I1=2I10=1D6=1I5=1D17=1I14=1D2=659N11=1D8=1I4=1D20=1D13=3I20=1I2=1X1=1X8=1I2=1I18=1X3=1D22=6I5=1I12=1D2=92N2=2I4=1X5=1D5=2I1=1X13=2D6=1I1=1X4=1D3=1I4=1I5=1I3=1D5=1D8=1I13=1X1=2I4=1D2=1I8=1D10=1D5=2I13=2X7=76S * 0 0 AAGCAGTGGTATCCACGGAGAGTACTTTTTTTTTTATTTTTTTTTATTTTTGTTGTTTCTCTGCTCAGTTCTTTAAGATTGGTGTGCCATTTCTCTGGAAGCCTCTTCAGAGAAGATCACGTGGCGCAGGCTGGGTGGAGTCCGTCCACCCATGGAGCACAGGCAGACAGAAGTTCCCCGCCCCAGACTGAAGTGGCCTCAGGCAGGCCTCTCGCTCGCTTGAAGCTGGTCTCATCCGCACAGTGCTGGGTTCCGTCACCCGCCAACCAGGGAAGCAGGTCCTTATAGCAGCCTTGTCCTGGCTTGTCATGTCAGAGCAATGGCCCAAGAAGTCTGGGTCTGTGGGGGAAGGATGGTCAGGAGCCCCCTACGATTCCGCATCGTCCTCGTCCTTCACTCTGCCTGTGGACGCTGCGGTGGCGGCAGAGGACGGGATGGAGTCGGACACGCGGGCAAAGCTCCTCCGGCCCCTCACAGCACCCCAGGATCCTAGTCTCCCCAAGAGAGGCCCTGCGCGGCGCTCATGCCAGCTTTGTTGAAGAGATCGACATCAAAGTCCCCACCTTGGCTCGTGGCTCTCACGTCTACCTGCTCCTTCTGCTTCGTCTTCTCCAAGCTTTCGCTCATCTATCACGCTGACGCAGCATTGCCTTGCCGATGCCCCCAGCTGGGGCGGATGGACCCCCTCCCCCACTTCCCTAGCAGAGTGCCCGGCCCACCGAGGGGTCGACCACTTCGCCTGGGAGCTCCCTGACTGAAGGAGACCGCTGCTGCCTGCGTCGTCCTGCCTGGCGCCTTGCCTACAGGGGCCCAAGCGGTTGAGGGTGGGAGTGGTGGATTCACTGGCCTAGCCACCTCAGGAGCTGGGGGAGGTGTGGGGGCGGTGGGGGTGGTGTGTGCTGTAGTACCCCCATCTTGTAGTCTGCTGAGTGGCTCGCTACCACACAGTGTGGAAGGTGCAGTTCCCGGAAGGTGGCCAGGGGGCAAGAGGGGCATGCCGGGTGCCCAGGTCGGCACTGAGTACTGTAGGTCGTTGCAATGCCGGCAGGTCACAGGCAGGTAGGACAGAACATCCCATATCGCAACACAAACGTAGATTGCATGGCTCACGAGAGCGAAAGAGCGTCGTGTAAGAACCGTAAGCGTGATT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SG:Z:MARS:1-25,Poly_A:26-58,cDNA:59-1072,BOREAS:1073-1085,UMI:1086-1095,CBC:1096-1111,VENUS:1112-1135,G:1136-1150 XQ:Z:0/0,21/26,0/0,0/0,33/46,24/32,41/50,58/60,0/0,22/26,0/0,0/0,27/46,24/32,38/50,56/60,0/0,23/26,0/0,0/0,36/46,13/32,39/50,60/60,0/0,26/26,0/0,0/0,35/46,27/32,31/50,54/60,0/0,26/26,0/0,0/0,37/46,24/32,40/50,46/60,0/0,14/26,0/0,0/0,33/46,18/32,28/50,56/60,0/0,21/26,0/0,0/0,36/46,26/32,40/50,60/60,0/0,22/26,0/0,0/0,24/46,28/32,37/50,48/60,0/0,26/26,0/0,0/0,35/46,26/32,44/50,54/60,0/0,22/26,0/0,0/0,35/46,24/32,31/50,60/60,0/0,24/26,0/0,0/0,39/46,17/32,40/50,56/60,0/0,23/26,0/0,0/0,30/46,21/32 +read_rev_5 16 chr1 14400 29 159S395=1I24=1D10=140N69=757N108=1I39=664N26=1I133=92N26=1D171=177N210=1I54=1I151=1X94=172N74=1I40=1I33=206N239=1I48=6183N154=4429N23=78S * 0 0 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCCTCACCAGCCCCAGGTCCTTTCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGAAGGAGACGCGCTGCTGCTGCTGTTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCTGGGGGTGGTGGTGGGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGTTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGCGAGCCGCCCTCCCGGAAGCCCCATATAAGAAACAGCGCCGCCACCTGTCTGGGTAGCAAGATCGGAAGAGCGTCGTGTAGAGATTGCGACCAAGTGT xIDO5V^}Iig[XcLWZTMVgVi`;Ffmoppppppppppoooi^foppppoonej+VYa\UM?3/.16>Q^ZTQOOQTW[_bddddaWNKNXbddb`][ZYYYTNLLMONFAAFLV^^\[\]`bddddddddddddddddddca^ZURONOV_dddddb_#_Fml20LUURYhTjXVxyEgy\YQrVxIcB6P~LU`kZ5UT>VmKS;SwAaXrSjRHaLMVWg6^yHZLO\[>H^]^4]aC\FvFXQa~~~~%Y\gBtbNa^h~WNm1^YbYnI]aln~0c~~~/Vb\sdmVi~6pCw[}QZ~KYb~N`Z~Me\w~N~Na~eG^t~SxJuRCpZsXoQkTZs~R~h~Pex_q~~~~5w~~B{evB{ZVqfuK:4KVd`M`f\xSMX|)s~VPheua^~6lkax_r[ecZb3X~Lw~6~a^e\r~~K[`j~~~~~}1v7pPMaiYYk~JXH~~~~'[^^ev~g~~Hp~,aCqLtbz\vbZZr^_^j[+P~_Cw6^u{3szM]}+0UNU&pNO}?_c~~~=^OP]~9_>JdqMKnbruf~}@gULUOT>PJNeMs~PdG\XNNdESWNanHrx~MfqLWVGlXbbH|}'i~M~f~T`w_eu~T\e[w_f\ibd\w~KufHx~8~gHjf\tbEVfUVNT^nN]c[oV%]e^w~Kvf^WXQ[rMYMJMAW~b~B~J|ff~Pe`A[rqxw9p`Sw^vS]{F]i~ToHx[vqd_rcqaq~S~l>jc~LaqP~Vt~{g-g[~AtLr]{U~~4t~|D_c[w~~CqM~b~TbYpJI0b>tfYlf[rfYPG|HP\upCL9;EMlU_f~N~FpS~?ur\Xkrp=~6e^~Md=Lu~rDf|vG\Ajnv~~?tfZMXXv=|Ptc_s|Ns_u~S\d\s~~s^;o~Ot{Sf_n~~+R\.Xsx{~+WyOQ?g8X_tc]l~-mx\~fes^s8Y=L[M[0tlK\w_~W\nRF;v_nbSed%r7r/OZj([bX~?[n~>wcs~RWP~M_~~~E^d^f~~~~?_~_WbwQ{~~>w~;U~NW2cNF{Wra^m^feeL~Om_e~`~BLp\[b~P`lC_q|QQFRS(_`~7Uk~Tuu~PsG]Yl_yex[gXr~;_^nOi~<[Z@Sw8][s~V_s_rjsc~T`^W[~U\t[k~~Ku}OufYgc~[~Hre\N\\_]r[cY{df[V3ZRcAtXpLbEZg,MaKZ~~EX_YWx9TvtM][set^m\ba~~~~d~Mn~~~~1p~8r~RjHcg_TCe]~e\gc[ss{KpeYK`Gf&^df0[?TMNc%UYX~E]xSc\cMv_s~xHJ@tex~9[bKaZW.*S[~1tJwAW~~DtZjfQ;V^lclb_'_e^qbEduf`s[[`i\P~4]~~EqpI~;\~~Eetb~@Yhc~Lr~~DYfFZ^z~|r,o~T^w~Kt~T~NvtuevfZ[Vn\wGr[kHn\ufhPa~hAg~q3MSex+dHu~Wc~:mU4~M~~:`5]w~CIcy=YYK}~~6eY~?i~Fuf~~3pZ_~W~DX\cBh~:|a\w]p7PvGk`~XbyQ[l[_q?\~c~@[b[ber`rct_~FamhbnPeZDho3pF^s~~~~3~Pcj~zAr\~h\ufX@E``PfBL^~~L\vdLtE[lf~SqTZ^^`Kd@MVXYq~@~~ZIE~7kh_rbI~P[_~Ouf[X~~L~~Ee^w_exy8Em~lb/]l7lb[gcfZo+p~SsvzOseu~K]~~~~:_ex\w[lf\X~U~QqYxEec_+S~~2_c~~Gbwe~H_tjuTsc~Msvr~hiLnf`p{(M]ao~'o~Arb[nGSE`CC|b~V`s]t~Sv`}5Vk[Go\^uu~L~J[PZ~feRge~~Axffux\u_Zt_~evH~`~=~Ks~~BvO~d~@tcuwKhbLJBug9xX_~S~;oSZn~;pxB@ob9p?Zc]b^<[?Lcp=pf\tchFacux~Mrft1]p~Ssc|?Z[Z]a^Zd\~T\rq~G\ug\w~~s>'>q4eBreNjZXvKrz&if]~A\_{[Dj`WpcsHXaIoEof.p6i~R~|DlMn~QN~R~~J\B~~~R~`~N{V?a{~X\l~plig~no~^l~~]~~\`[k~n~~M~~ntq~omlk~^l~^~~Ebgl~n~~~PRoa~~~~|~&~u~Lvp~rvt~G~k~~~~1rwpq~~]~~>clzYp}x1~?kj~Z~~Y[Ngn~]u@v~_m~qo~qm~Qr~E\}Q^n^l~F~~~S~~~^~JbT~g}qzqnft~n~~P~\k~~[R~M~~Rm~gEjq~~\qm~~~@~~\~~]~~P~~Erg{m}ji~~L~_lpT~M~q~r?~~_~Qo~sp~^L~cm~m~~~\Y|Ye{k~7Z\I~~Aj~Z{l~Tp~qdR~TZYl~q~l~tqZw~DupN~~J}sT~qf|^P~qQ~YB~~Nh8l~~ipqm~~\sbpv_fOzRfojkhb~s~\~_~sq~Vpx~pn~~$gen~X~_p~Qf_~0[T~mmTaq~akh~~_~~Snm~[t~T~[j~~~0gn~cv[~faj~~Jg~~JymC\~~M~~\bi|q~p~Z~o~pqqqo~gj~qm~pJQYyqp~~6~`~]x~D^iuH~Z~Y~]jpj~JR|%~[g_~CW]=qZc'^zj>d0Z\Nh{.8gjUe~oT~\}VXg~Mtq~~I~pmh~t=b2\s6c~T}kPur,c~X~~~~~6]~Y~o~j~m~g~~~8vnm~sqy_~\~n~iX|`}~7mlf~XQmy~UsfOe\i~~\~Q~S~~~@fsl~qmg~N~SW~Aqq~Vqr~~HWccr~~~~/o~jieh*~~~K~~O~kGgp~[C~fbnnthP]i~~Uppp~t~\p~ieE=U~~.Yk~Unqw~]qz~S~~~ZmJ~A~dm~~q~t~ctry~Zq~~^q}H~tKd~]~Tz~EFfft~~o~tgTth}Sn~o{~~@e}OYlm~p~v~_~mmgbj~m~Y~m~sqo~q~~~\wj~t~~~~.q~~a~~_a~Gl~]m~~Y~j~p~b~[xUy~~~?~mcdpIh]XU~~O~T~~hp~k~mzbq~~^~m~_~~~x~.~~\~~Z~jmtp|x~m~um|cn~~q~~FvKoqqr+{~D[`{Tk|adnlji@m~as4~mmw?~lillPm~p}~d~Njd~~~P~fm~~~~t3le^f~i4q[y~,k~jqqUm~~[fdy<^Y~_~~~Oo/bj~`_j\ipj~E~m~~q~\~Paymqn}h\z]P^m_XDf~j~tm~F~tl{~p SG:Z:MARS:1-25,Poly_A:26-95,cDNA:96-1310,BOREAS:1311-1324,UMI:1325-1334,CBC:1335-1350,VENUS:1351-1373,G:1374-1389 XQ:Z:32/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,44/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,50/60,0/0,26/26,0/0,0/0,42/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,52/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,52/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,42/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,42/60,0/0,26/26,0/0,0/0,44/46,30/32,45/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32 +read_rev_8 16 chr1 14400 18 98S194=1I236=140N69=757N108=1I44=659N159=92N198=177N87=1X48=237N74=78S * 0 0 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCTGGGGGTGGTGGTGGGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTTTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCCCCATATAAGAAAGAGGTGCCTCCCAGACTCTGTAGTGGAGATCGGAAGAGCGTCGTGTAGATCGGACCTGACAGAGT ~yqu~lr|J~l~~~\}~~|fZU~vhgtms~~~~~~~~~~~~~~~~~}xtdaht~x+Zq~~~}~~~~~~~~wmfcejt{}~||~~~~~~~~~ym`YYc~~&{k~~S~~~~~~w~~ag~~Zw~d~~~x~Xx~~~~a}uz~'i|l^~e~Xq~S~~{o~e~~h~{n~~~~E~~~r~H~~wrJj~[wo~Z~~~~~~~@~~~i~nSXot~W~~~Y}}qvb~~~~~Kf~~~U~xD~`b_{~f~M~~~av~d~l~m~w~\~~~~cth~~a~~~~Y~[i~m~~~f~yv~~~~M\B~Zj~~qRM~~~1{~~O~n~b~X~{jsa~g_~}b~~~~~p~~~b~~k~obilj~GyRd~~~{uzl~3r~i~~]~|a~|u~~ZTwoeu~~~~2~h~l{{zywO~]~l~sq~MukL~~~Y~_1o_`wux~U~~~~~bw~e~}~~~f~~z~_c~r~~~~~ny~]~~Y~v~s~c~~~Bq`iK~~~~t~zjhr~g~~U<[~\~fpdoCq~YkkHy~~S~~_}Y~~~~~V~~h]~^}~W~~Rphigjl~~~[n]}~l~`Zhhmg`~h~zf~\~~mh~\~~h~f~K[~~}v~z:Mu~~~Yb~U~n~OC}on~~d~v\wT~|sar~~~mzz}t~\~h~mj~tyc~~~~W~s~Jw~c|~^kg~v~Y~j~~~~t~qo~y~~~~h~Z~n~}~~^llp~~~~~Ku~z~i~_Z~\~~~^~a~t~~~~~~~~~~Ew~Rp~~g~~a~I~~~~Jym~e~W~~~a~~`~~~DHj}y~~@~~V~~~~~f~X~Nyp~~z~~~~~~v~h~~oygx~~fZq~h~~\~~~m~s~J~Kvk~~~~~J~^u~~k~bjt~~\f~~Z~tp~~~~:y~~vy~~W~]~clh~Jttb~Y~~cfw~f{B~~^~~Zb~~~~A~~aFl~gv=~~`ph~`~`uoxW_@Latpn~|^~b~|uc~~h~~j~~~~oli~~k~zo{w~n~[~v{Ai|~O~~mvW~p~]~_n~T^v~Xw~~~G`b~~~~~~B~~smZ~Y~~~S~~M~~[~p~h~~l~tjoyZq~~~hi~~~b~n~QL|~~/~~K~~~jyhs~by~~m~~~[~~~n~_wp~~~}~~~~z~U~~~kr~T~~Qg~m~g~~_~~~~~~~~k~~~y~Yr~qXrwBz~d~~~~~~\~1~q~r~t~~~y~y~Zlput~~~Ei}~}~~~~K~~~~~~6k_t~~hg~uT~~~~~K~~c~~~~~;qous~]Vs~~~~O~~~~Jc~v~~~n~h~\x~~Zs~~~~B~~Ov~apP~~~~~~c~^~~n~ru~~~e~f~~mr+q~jth}M~yUsnhc~~~~|~Xz|~~~z~~~~~~y~~or~t~b~~~V~sRxz~~~3~wwr~~J~~fp.~~~~~I~~~>ck~VfDzax~~M~}{t~g~~yy~y~X~~~~~~b~mZtnyf~~~~~~z~cYv~ch~Yr~~~~fuww SG:Z:MARS:1-25,Poly_A:26-100,cDNA:101-1317,BOREAS:1318-1331,UMI:1332-1341,CBC:1342-1357,VENUS:1358-1380,C:1381-1396 XQ:Z:32/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,39/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,52/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,46/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,24/26,0/0,0/0,44/46,30/32 +read_rev_9 16 chr1 14400 1 63S4=1I10=1I17=1X4=1X5=1I7=1X4=1X1=1X2=1I2=1X8=1X2=2D1=1D10=2X8=1D6=1I5=1D18=1I6=1I5=2I3=1X4=1D4=1X3=1I2=1I1=1X13=2I1=1X5=2I6=2I8=5I5=1X4=1I1X5=1X5=1I31=1X5=1X5=1X1=1X3=1D11=1X10=1X5=1I8=1D9=1D6=1I15=2I6=2I28=1X4=88S * 0 0 AAGCATGCGGGGTATCAATCCAGAGTACTTTTTTTTATGATTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTCTGCTCATGTTCTTTATTGATTGGTTTGCCATTTTCGTCTGGAAACCTCATCAGAAAGACAGTGGCTCACGGGTGGAGCCTCCCCCCCATGAGCACTAGGCAACAGAAGTCCCCGCCCCAGGCTGTGTTGGCCCATCAGGCCACCTTGCGCGTCTCATGAAGCTGGTCTCCGCGCACAGGTTGCTGGTTTTCCGTCACCTACCCCCCACCCAGGGGAAGCAGGTCTTGAGCAGCTTGTCCTGGCTGTGTCCATGTCATAGCAATGGCCCCAATCTGGTCTGGGGGGAAAGGTGTCATTGAGCCTCCCTACGATCCCAGTCGCCTCGTCCCTCCTCTGCCTGTGGTGCTGCTGAGCGGTGGCGGCAGAGGAGGGATGGAGTCAGACATGCCCCATAAAAGAAACCAATTCTTCCAACCAACACCTTAACTGCAGTGATCGGAAGTAGCCGTCGTGTAGATCTTCACAAGTAAGCT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SG:Z:MARS:1-28,Poly_A:29-61,cDNA:62-459,BOREAS:460-473,UMI:474-483,CBC:484-499,VENUS:500-529,A:530-545 XQ:Z:34/50,58/60,0/0,21/26,0/0,0/0,38/46,24/32,42/50,60/60,0/0,26/26,0/0,0/0,40/46,26/32,45/50,58/60,0/0,26/26,0/0,0/0,32/46,28/32,41/50,60/60,0/0,26/26,0/0,0/0,44/46,20/32,36/50,60/60,0/0,26/26,0/0,0/0,42/46,28/32,36/50,56/60,0/0,19/26,0/0,0/0,46/46,19/32,41/50,50/60,0/0,26/26,0/0,0/0,43/46,32/32,39/50,57/60,0/0,26/26,0/0,0/0,41/46,20/32,48/50,52/60,0/0,26/26,0/0,0/0,39/46,23/32,43/50,60/60,0/0,22/26,0/0,0/0,23/46,25/32,38/50,60/60,0/0,18/26,0/0,0/0,40/46,19/32,43/50,60/60,0/0,23/26,0/0,0/0,44/46,22/32,31/50,52/60,0/0,22/26,0/0,0/0,38/46,30/32 +read_rev_10 16 chr1 14404 15 175S426=140N69=757N110=85S * 0 0 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCAGCCACCCCATATAAGAAAGCATAGCGTTGTCTTTAACACTGCGCAGATCGGAAGAGCGTCGTGTAGAAGGCTCTGATCTAGGT ~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~$~~~~~~~~~~~~~d~~~~~~~~_~x~v~~~~~~k~~~~~b~~~~~~~~~~}~~~~~~~~~~O~~~~~~~~~~f~~pk\p@~~~~~~~<~~~~~~~~~~~1~~{~~~~~~~~~~~e~~~~m~~w~~~r~~n~~~~~~~~~~~~f~~~k~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~f~`~~~~{~~~~~<~~~E~~~~~~~~~~W~~~~~~~~~~~~~~~R~~v~~~~~~~q~~~~~~~~~~~z~~~~~>~~~~~~~~L~~~~~~~~~:~~~j~~~~~~~p~~~~~~`~~~~~~v~~X~~~~~~~~~y~~~~~~~~~~~~~~~~~W~~~~~~~~~~~~~~u~~~~~~~~~n~~~y~~~~~~~~~~~~~~R{~~~~~c~~m~~b~~r~~~[~~~~~~~~~~g~~p~~s~~~~~R~~~~~~~~~S~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~w~~n~~x~~~m~~~~~~t~~~~~~~~q~~~~s~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~a~~~~~~}~~r~~~s~~~~~~~~~~~~~~i~~i~~~~~~~~l~~~~~~~~~x~~~~~o~~~~~~~~~q~~~~~~`b~r~~~~~~~~v~~~~~~~~~~~~p~}~p~~b~~~~~~~~~~ SG:Z:MARS:1-25,Poly_A:26-175,cDNA:176-786,BOREAS:787-800,UMI:801-810,CBC:811-826,VENUS:827-849,M:850-865 XQ:Z:32/32,48/50,54/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,50/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,52/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,54/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,56/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,58/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,44/60,0/0,26/26,0/0,0/0,44/46,30/32,48/50,60/60,0/0,26/26,0/0,0/0,44/46,30/32 +read_fwd_1 0 chr1 632482 1 69S3=1X3=1X3=1X1=1I18=2I48=1I1=1X15=1I1=1I2=5I4=1I1=1I3=1I3=1I4=3I4=1X1=2I5=2I4=1X1=2I1X3=1I4=1I2=1I7=1I6=1X4=1X6=1I5=1X2=1X1=1D8=1X17=1X5=199S * 0 0 AGAGTCCTAATACGCAGTCTACACGACGCCTTCCGATCTCCGGTATTGCAATACGCTGGGTGAATCCTATTCTTAAATTGGGAAAGCCTTCGCTTCGAAGCGTGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATAAAGGATGCCCCCCACCCGTAACGGTGGCACATCGATTACGATAGAATAGCCCGAAATTACATTAAAAAGCAACAGATCAAACAACAGGAAGGAAATCGACCCCCTCAAAGCGTGGTTCCATGCAACCCCAAGGCCTCCATGACTTTTTAAAAAATAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAGAAAAAAAAAAACAAAAAAAAAAAAAAAAAAATAAGAAAAAAAAAAGTACTCAGCTATGATACACTGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,10/26,0/0,56/60,42/50,27/32,35/46,0/0,0/0,23/26,0/0,56/60,40/50,23/32,41/46,0/0,0/0,17/26,0/0,60/60,31/50,22/32,35/46,0/0,0/0,26/26,0/0,58/60,35/50,20/32,40/46,0/0,0/0,24/26,0/0,50/60,41/50,18/32,35/46,0/0,0/0,26/26,0/0,58/60,29/50,22/32,34/46,0/0,0/0,26/26,0/0,56/60,39/50,22/32,41/46,0/0,0/0,20/26,0/0,60/60,34/50,13/32,39/46,0/0,0/0,24/26,0/0,58/60,35/50,27/32,40/46,0/0,0/0,22/26,0/0,60/60,34/50,23/32,41/46,0/0,0/0,19/26,0/0 SG:Z:F:0-16,VENUS:17-40,CBC:41-56,UMI:57-66,BOREAS:67-82,cDNA:83-299,Poly_A:300-480,MARS:481-504 +read_fwd_2 0 chr1 632508 1 83S22=1D13=1I16=1I2=1I11=1I11=9I6=1X5=1D7=1I33=1I16=2X20=1D17=267S * 0 0 ACCTCCCTCCCTCCAGAAAATCTACACGACGCTCTTCCGATTCTTGCGCAGCCATTGGTACCGTAGCCGTTTTTCTATATGGGGAAGCGAAAAGTCCTAATAGTAAAGAACCCTCCATAAAACCTGGAGTGACTATTACTGGATGCCCCCACACCCTACCACATGACAGCGACATTCTAAGAACCGTATATCATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCCAAAGCTGGTTCGAAGCCAACCCCATGGCCTCCTGACTTTTTCAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAGTACTCTGCTTTGATACCACTGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:32/46,0/0,0/0,26/26,0/0,58/60,48/50,26/32,43/46,0/0,0/0,21/26,0/0,60/60,44/50,21/32,32/46,0/0,0/0,21/26,0/0,46/60,44/50,30/32,33/46,0/0,0/0,26/26,0/0,58/60,47/50,28/32,34/46,0/0,0/0,23/26,0/0,54/60,44/50,26/32,33/46,0/0,0/0,17/26,0/0,50/60,42/50,24/32,36/46,0/0,0/0,26/26,0/0,60/60,43/50,27/32,38/46,0/0,0/0,20/26,0/0,54/60,40/50,27/32,25/46,0/0,0/0,26/26,0/0,58/60,45/50,25/32,46/46,0/0,0/0,21/26,0/0,58/60,35/50,17/32,46/46,0/0,0/0,26/26,0/0,58/60,44/50,17/32,35/46,0/0,0/0,26/26,0/0,56/60,45/50,28/32,42/46,0/0,0/0,26/26,0/0,60/60,32/50,25/32 SG:Z:D:0-19,VENUS:20-44,CBC:45-60,UMI:61-70,BOREAS:71-83,cDNA:84-272,Poly_A:273-521,MARS:522-546 +read_fwd_3 0 chr1 632510 1 84S19=1I11=1D6=1D4=1D20=1I1=1X21=1D7=1I14=1I25=1I13=1X16=1I11=1X6=1X1=1X2=1X1=1X5=205S * 0 0 AGTGTACAATTCAGCAGTCTACACGACGCTCTTCGCGATCTAGTCTTTCACCAAACGCGCGTTTATACCTGTTTCTTATAGGGGAGCGAAAAGTCCTAATAGTAAGAAGAACCCTCATAAACTGGGTGACTATATGGATGCCCCCACCCCCTACCACACATTCGAAGAACCGTATACCATAAAATCTAGACAAAAAAAGGAAGGAATCGAACCCCCCAAAAGCTGGTTTCATGCCAACCCCATGGCCTCCCATGACTTTTACAAAAAAAAATAATAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAGTTACTACGGCGTGATACACTGCT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,14/26,0/0,58/60,43/50,19/32,43/46,0/0,0/0,23/26,0/0,54/60,45/50,30/32,36/46,0/0,0/0,22/26,0/0,60/60,41/50,30/32,34/46,0/0,0/0,22/26,0/0,54/60,46/50,25/32,41/46,0/0,0/0,21/26,0/0,44/60,40/50,19/32,43/46,0/0,0/0,22/26,0/0,60/60,27/50,23/32,33/46,0/0,0/0,21/26,0/0,58/60,47/50,28/32,42/46,0/0,0/0,24/26,0/0,60/60,40/50,30/32,38/46,0/0,0/0,22/26,0/0,60/60,50/50,30/32,44/46,0/0,0/0,23/26,0/0,56/60,45/50,26/32,35/46,0/0,0/0,26/26,0/0,57/60,43/50,30/32,26/46,0/0,0/0,19/26,0/0 SG:Z:F:0-16,VENUS:17-41,CBC:42-57,UMI:58-67,BOREAS:68-84,cDNA:85-261,Poly_A:262-460,MARS:461-484 +read_fwd_4 0 chr1 632519 1 95S8=1I1X2=1D8=1I5=1I7=2X2=1I9=1X2=1X16=1I16=1I2=1D4=1X4=2I10=1I13=3I37=1I19=1X1=1X1=1X2=1X5=90S * 0 0 AGTGCGTTTTGCGAATTGTCTACACGATACCCTTCCGATCTCCAAGTTGCAAGTAGTACAGCACTGATTAGCGCTTTTCCTCTATATGGGACAGCTCCTAATATATAAAGAACCCTTCCATAAAACCTGACGTCGACTATATGTATTCCCCCCACCCTACCACAACATTCGAAGAACCCGATAACATCAAATGCCTAGACAAAAGAAGGAAGGAATCGAAAAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCGTCCATGACTTTTTCAAAAACAAAATAAAAAAAAAAAAAAAAAAAAAAAAAATGACAACTAAAAAAAAAAACAAAAACAAAAAAAAAAGGACTTCTAGTCGTGCGATAACCACTCTCGCACTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:28/32,40/46,0/0,0/0,24/26,0/0,57/60,40/50,27/32,36/46,0/0,0/0,26/26,0/0,56/60,42/50,22/32,29/46,0/0,0/0,26/26,0/0,54/60,35/50,22/32,43/46,0/0,0/0,20/26,0/0,58/60,43/50,28/32,28/46,0/0,0/0,23/26,0/0,46/60,39/50,30/32,28/46,0/0,0/0,26/26,0/0,44/60,34/50,24/32,37/46,0/0,0/0,19/26,0/0,52/60,28/50,26/32,41/46,0/0,0/0,22/26,0/0,54/60,44/50,26/32,34/46,0/0,0/0,20/26,0/0,57/60,20/50,24/32,40/46,0/0,0/0,23/26,0/0,57/60,32/50,30/32,35/46,0/0,0/0,26/26,0/0,46/60,39/50,14/32,36/46,0/0,0/0,18/26,0/0,54/60,35/50,22/32,29/46,0/0,0/0,26/26,0/0,48/60,27/50,24/32,29/46,0/0,0/0,19/26,0/0,32/60,38/50,23/32,28/46,0/0,0/0,24/26,0/0,36/60,23/50,18/32 SG:Z:I:0-17,VENUS:18-41,CBC:42-57,UMI:58-67,BOREAS:68-90,cDNA:91-272,Poly_A:273-345,MARS:346-380 +read_fwd_5 0 chr1 632563 1 79S11=1X4=1I17=3I17=1X11=1X14=1I4=1I19=1I1X5=1X1=1X6=1X5=1X2=1X1=1X1=1X6=97S * 0 0 ACTCGGTCAGGTCACGATCTACACGACGCTCTTCCGATCTGCTACCATCCGCAGTGTCAAGATCGATTTTCTGATATGGGGATGCCCCCCCCCCTAACCACACATTCGAAGAACCCCCCGTATACATAAAATCGAGACAAAAAAGTAAGGAATCGAACCCACCCATAAGCTGGTTTCAAGCCAACAACCATGCCTTCCATGCCTTTTGCATATATATATTAATAAAAATTTAAAAATAATAAATAAAAAATAAAAAATTAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAGTACTACTGCGTCTGATACCACTGCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:31/46,0/0,0/0,21/26,0/0,53/60,43/50,17/32,44/46,0/0,0/0,21/26,0/0,50/60,40/50,23/32,46/46,0/0,0/0,22/26,0/0,57/60,42/50,26/32,39/46,0/0,0/0,26/26,0/0,52/60,35/50,30/32,37/46,0/0,0/0,22/26,0/0,60/60,44/50,22/32,33/46,0/0,0/0,22/26,0/0,58/60,32/50,25/32,33/46,0/0,0/0,24/26,0/0,56/60,32/50,22/32,33/46,0/0,0/0,20/26,0/0,50/60,39/50,25/32,38/46,0/0,0/0,26/26,0/0,50/60,35/50,21/32,37/46,0/0,0/0,26/26,0/0,58/60,31/50,26/32,26/46,0/0,0/0,26/26,0/0,52/60,36/50,23/32,31/46,0/0,0/0,26/26,0/0,54/60,37/50,27/32,30/46,0/0,0/0,19/26,0/0,57/60,50/50,22/32,39/46,0/0,0/0,26/26,0/0,58/60,38/50,24/32,23/46,0/0,0/0,26/26,0/0,60/60,42/50,32/32 SG:Z:C:0-16,VENUS:17-40,CBC:41-56,UMI:57-66,BOREAS:67-80,cDNA:81-230,Poly_A:231-290,MARS:291-317 +read_fwd_6 0 chr1 632750 1 94S3=1X2=1X7=1I1=1X11=1I6=1I4=1X9=14I9=1D1=1X4=1D7=1X7=1D6=2I3=1X19=2X9=2I3=1X1=1X1=1D5=1I17=4I6=1I5=4I4=1X5=2I4=1X20=1D18=1I6=2I5=1X4=2X2=1X35=1D17=1X6=1D10=1D1X3=1X7=1I2=1I9=105I5=1X1=16I2X2=3I1=1D3=2I13=4I3=1D1X1=1X2=1X2=1I1=1X2=20I5=1I7=1I3=1D27=1I9=1D13=1X10=1I11=1X7=1X9=1D3=1X9=1D19=1D6=1D15=1D7=1X3=5I12=9I5=2D3=1D1X6=1I7=1X3=2X4=1D11=1X1=1I5=3I5=1I1=1I7=1X1=1D19=1D2=1X4=1X5=1X2=1X6=1X19=1X3=2I5=59S * 0 0 TATATGTGTATATCTGTGCTTACGCTTTCAGGCCGATCTACACTACCAACTTCCGTATCGGTCCACTAACCACAATTCAATGAATTGATTTCCTTATATTGATGGCACTAAGCAGCGCAAGTAAGGTCTAACAATACGCTACTTGCCACCCCCCACACCCCCTATCAATAAGACTTATCACCTTTCATATCACGCACCCACATAATCATTTTCCTTATCATCTTCCTAGTACCCTATGCCCCTTGTTCCTAACACTCACAACGAAAAAAACTGAACTAAATTATACAAACATGACTCACACGCTCAGGAAATAGAAACCTCTGAACTATCCTGCCCGCCCATCATCTCCTATTCCTCTTCCCCCTCCCATCCCTACGCATCCTTTACATAACAGACAGGTCAACGATCCCTCCCTTACCACAAATCAATTTCCACCAATGGTAACTTGAACCTACAGTAAGAAGGGGGTTGGGGATTGTGGAGTGTGAGGGGGGGGGGGTGGGGGGGGGGGGGGGGGTAAAGGGGGGGGGGGGTGGGGGGTGGGGGGGGGGGGGGGGGGGGAATATATATAGGGGGGGGGGGGGGGAAATCACGACGCGGACTAATCTTTAAACAAACATAAATAAGTTGGGGGGGGGGGGGGGGGGGCCCCCCAATTATTCACTAAACCAGGCGACCTGCGACTCCTTGACGTTTGACAATCAGTAGTACTCCCGATTGAAGCCCCTCATTCGTATAAAAATTACAACACAAGACGCTTGCACTCATGACTGTCCCCACATTAGGCTTAAAACAATGCAATTCCCGGACTCTAAACAAAAAAAATCCACTTTCACTGGGTGCATGCCTACAACCTGGGTATAACTACGGTCAAATCTCTAAATCTGTGGATCAAAACCACAAGTTTATCATGCCCAACTCCTAGAATTAATTCCCCTAATATCTATGAAAAAGAGCCCGTTTTTACCCTATAGCACCCCCACTAAGCCCCCACATAAGCCAAAAAAAAAAAAAAAAAAAAAAAAGTACACTGCGTTGTATACCACTGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:29/32,41/46,0/0,0/0,21/26,0/0,60/60,41/50,30/32,30/46,0/0,0/0,20/26,0/0,57/60,32/50,17/32,25/46,0/0,0/0,17/26,0/0,46/60,41/50,28/32,33/46,0/0,0/0,18/26,0/0,42/60,24/50,24/32,37/46,0/0,0/0,26/26,0/0,46/60,33/50,28/32,37/46,0/0,0/0,16/26,0/0,50/60,28/50,22/32,20/46,0/0,0/0,19/26,0/0,52/60,17/50,27/32,32/46,0/0,0/0,22/26,0/0,58/60,25/50,27/32,34/46,0/0,0/0,19/26,0/0,54/60,39/50,26/32,25/46,0/0,0/0,18/26,0/0,54/60,35/50,23/32,28/46,0/0,0/0,21/26,0/0,48/60,41/50,19/32,25/46,0/0,0/0,18/26,0/0,44/60,42/50,20/32,46/46,0/0,0/0,13/26,0/0,60/60,44/50,30/32,33/46,0/0,0/0,7/26,0/0,44/60,38/50,28/32,25/46,0/0,0/0,26/26,0/0,60/60,26/50,16/32 SG:Z:C:0-35,VENUS:36-61,CBC:62-77,UMI:78-87,BOREAS:88-102,cDNA:103-991,Poly_A:992-1024,MARS:1025-1050 +read_fwd_7 0 chr1 632756 1 77S38=1D26=1D1=1X24=1D4=1X15=1I3=1X2=1I1=1X1=1X6=1X2=1I6=1D13=1X4=1I28=1D11=1X7=1D9=1I10=1X8=502I7=382N3=1X7=1X2=1X3=2D22=2I10=1D3=1X6=1I9=1X2=1X3=60S * 0 0 AGAGGTCAATTCGCAGTCTACACGCGCTCTTCGATCTTGACAACCTAATATCGAGTGTATGGTCTTTTTATATGGGGAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTATTCCCCTATCATAGAAGAGCTTATCACCTTCATGATCACGCCCTCATAATCATTTCATTATCTGCTTCCTAGTTCCAGTCATGGCCTTTTACTAAACACTACAACAAAACTAATTAATGACTAACATCTCAGACGCTCAGGAAATAGAACCGTCTGAAATATCCTGCCGCCATCATTCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAAAGACGAGGTCAACGATCCCTCCTTACCATCAAAATACTCATGGTCAACCAATGGTACTGAATCCTCTGAGTACACCGACTACGGCGGGATAAGTTTCAACTCAACATACTTCACCCTCATTACTAACCTTAGAACCAGGCGCTTTGCGAACACAAATCCATAATACCCCCACCCTCTAACTACACCCAATCCACTCCCACAATACACAACCAACCCACCCTCACTAAATCACATCTCATTACCAAAACTTCCCAACCCCCCCTTCATCCAACCTTCCTACACCCCTCCACCCAACACCCTCACACCCTACATTATTATTCACCATCCTTCCACCCCCCCCCCCCATTCCTCCCCCCTTCTCTTACTTAACAACCCACCCCGCCCCCCCCCCCCCCCCCTCCCTAATTATATGAAAAAACACCCGCCCCCCCCCCCCCCCCTCGTCCAACAATCCCCCCCCCCCCAGTTTTCCGCCCCCCATCCATCTTCCTAGATTTTATTCCTAAAAATCTTTGAAATAGGGTACCCGTATTTACCTTTAGCACACCCCTCTACACCTTCTTAGCATGCTCATCAAAAAAAAAAAAAAAAATGTAAACTCTGCGTTGATATCCACTGACTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,10/26,0/0,54/60,34/50,21/32,29/46,0/0,0/0,22/26,0/0,46/60,40/50,15/32,37/46,0/0,0/0,26/26,0/0,46/60,43/50,25/32,40/46,0/0,0/0,22/26,0/0,60/60,40/50,25/32,35/46,0/0,0/0,22/26,0/0,50/60,39/50,22/32,36/46,0/0,0/0,21/26,0/0,34/60,38/50,21/32,35/46,0/0,0/0,22/26,0/0,57/60,36/50,27/32,36/46,0/0,0/0,26/26,0/0,36/60,33/50,24/32,39/46,0/0,0/0,23/26,0/0,50/60,36/50,27/32,39/46,0/0,0/0,20/26,0/0,34/60,27/50,19/32,40/46,0/0,0/0,15/26,0/0,44/60,33/50,27/32,38/46,0/0,0/0,17/26,0/0,40/60,48/50,16/32,37/46,0/0,0/0,22/26,0/0 SG:Z:F:0-15,VENUS:16-37,CBC:38-53,UMI:54-63,BOREAS:64-76,cDNA:77-898,Poly_A:899-928,MARS:929-957 +read_fwd_8 0 chr1 632756 4 102S8=4I15=2X33=1X6=1X1=2I11=2X3=1X3=2I1=1I5=7I9=1I12=1I6=1X4=1D12=1I6=1I22=2X35=1X21=1I1X9=4I4=4I6=1I5=4I12=1I1X7=2I13=10I1=3I2=3I3=1I8=4I9=1X10=1I5=1I3=1D1=1X3=1I3=1X1=3I2=2I2=1I7=1X11=8I16=7I7=3I5=20I2=3I7=3I5=4I3=1I8=1I6=5I10=100I8=1X6=10I7=4I22=1D2=1X2=1X1=1X3=1I4=1I14=1X2=1D9=8I2=1X13=2I6=27I7=25I2=11I9=14I1=4I5=3I6=1X1=1I4=2I6=1I3=1D4=1I3=1I20=4I7=1I3=1I12=1X6=4I7=6I28=1X3=280S * 0 0 AGTGCGTTGCGAATTGTCTACAACACGAAACCAGAAACGAACGCTCTTCTCCGATCCTCCATTCGTATCGTCCACAGTCCCTGGCTCGTTTTTCTTATATGGAATGGCACATATATGCAGCGCAAGTAGTCCTACAAGACGCTACTTCCCCTATCATAGAAGAGGTTATCAACCTTTTCATGATCAACCCCCCATCCATATCATTTTCAAGTTTCCTTATACTGCTTCCTAGTCCCTGTATGCCCTTTCCTAACACTACACAACAAAAACTAACTAATACTAACATCCAAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCAGCCCGCCATCATCCTAGTCCTCAATCGCCCTCGTCTCCATCACCCCCTACAGCATCCTTTCTTTACATAACACAACGAGGTCACAACGATCCCTCCCTAACCCCTATCCCTTGAAACCGATCAAATCAAGAAATTGGCCACCAATGGTACTCGAACCATACAGTACAACCAACCCCTAAACGGGCGGACAAATCTTCAACTAAACTCCCCCTACATACTTCCCCCCATAAATATTATTCACGCTAGACCCACAAACCGCCCAAAAACACAAGCAGGCGAACCCCTGCGAGAGACTTCCTTGACGGTTGACAATATAATCGAGTAGGTACTTCTTTATTCTATACTACTTTACTACCGCTCTCACTTTACTAACTCCCCGAATTGAAGCCCATAACTCTGCCATTGTACTTTGGTACTATCTCTACTACTCCCGATTGAAGGCCCTGAGCCCCCCCATTTAATCGTATAATAATTACATCACAAACTTCGTGCACATCATAGAGCTGTCCCCACAATAGCTTAAAAAAAAAAAACCATATGCAATTCCCGGGAACGTCTAACCAAAACACACTTTCATTCACCCACAAACCAATTCACCTCCATCCCAACTTTCCATCACCCGCATCAAAACACTTTCACATATTTCAAAACATTCACCGCTACAAAACGACCGGAGGGTAAATACTAGCGGCAATGGCTACTGAAATCTGTGGAGCAAACAACACAGTTTTCATGCCCCATCGTCCTAAAATTAATATTTTCCCCTAAAAAAAAAAATCTTTGAAATAGGGCCCGTATTTTCCCCCCCGTATTACAACCCTATAGCAAGATAGCACCCCCTCTATAAATCTCTCTACCGCCCCCCGCAAATCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAACAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTACTCTACTCGACTCTGCGGTTATACCACTTAGGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:22/32,38/46,0/0,0/0,21/26,0/0,60/60,31/50,25/32,27/46,0/0,0/0,10/26,0/0,58/60,38/50,32/32,33/46,0/0,0/0,19/26,0/0,58/60,45/50,32/32,38/46,0/0,0/0,23/26,0/0,48/60,33/50,22/32,36/46,0/0,0/0,26/26,0/0,56/60,45/50,17/32,34/46,0/0,0/0,26/26,0/0,60/60,40/50,26/32,30/46,0/0,0/0,23/26,0/0,50/60,36/50,30/32,34/46,0/0,0/0,23/26,0/0,60/60,36/50,32/32,27/46,0/0,0/0,24/26,0/0,60/60,31/50,27/32,21/46,0/0,0/0,9/26,0/0 SG:Z:I:0-16,VENUS:17-58,CBC:59-74,UMI:75-84,BOREAS:85-103,cDNA:104-1197,Poly_A:1198-1371,MARS:1372-1408 +read_fwd_9 0 chr1 632757 1 81S21=1D42=1X5=1I9=2I8=1287I3=8D1=1X19=1X1=1I22=2I16=1I16=1X8=1I6=1I13=1I7=1I1X4=1X8=1X2=1X36=1I6=1D3=1X7=1X8=2I7=2I7=1X13=1D6=1I1X1=1X17=1X13=79S * 0 0 AAGGTCACCGGCACATTTCTACACGACGCTCTTACCGATCTTTGCTGCTCAAGCTGAGTTGCGTTTTATTTCTTATATGGGATGGCACATGCAGCGCAAGTAGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCAATGATCACGCCCCCTCATAATCATTTTCCCTATCCTCCATGCCCATTAGGCCCCTTCCTACCCCCCCTCACAACATACTACCCTATACTAACACCCCACCCTCAGACAACCTTCCCCCCCCCCCTTCCCCCCCCATCATCCCCTAGTCCCCTCATCGCCCCCCCATCCCCTACCCATCCCTTACATACACAGCACACCCTCCCCTTACCCCCCCCCCTCTCTCCCCATGCCACATGCCCCCCCACTCCCCTCTGCCCTCTCCACCCCCCCCCCTCCCCCCTGTCCCCCCCCCCTCCCCTGCCTCACTCCTAAAATCCCCTCCCTCCTGCCCCCCTCCCCTTTTCTCTCCTCTCTCCCCCCCTCCCCATCTAAATCCCTCCCCCCGCTTCCCCCTCCTTTCCTTCCCCCTTCTCCTATCATTCTCCCCTCCCACCTCCCCCTCATCCCCTCCCCCCCCCCCCCCCGCTCCCCCGCTCTCCTCCCCCTCCCTTGCCCACCCCACACTCCACCCCCCCCCCCTTTCCGCACTCCTCCCCTCCTCTGTTCCACTCCCCCACATGCCCTCGCTCTCTTCCTCCTTCCAATCCCTCCCCCATCCCCCCTCTCCCCTCCTTCCTGCCCCCCCCCCCCTGCTCAACTCACTCCTGTCCCCCCCCCCTCCTCCCCCCCCCCCCTCCCCTTTTTTTCCCCTCCCCCCCCCCCCCCCCCCTCTCCTCCCCCTCCCCCCCCCCCTCTTCCCCCTCCTCCTGGGTTTTTTTTCCTTCCCTGTCTCCCCTCTCCCCCCCCCTCCCCTGTTCCCTAATCTCTCCCCCTCCCTTCCTTCTCCTCTCCCCCCCCCTCCCCCTCCCTCCTCCCTCTCCTCCCTATCCCCTCCTTTCCTCCCCACCCTCCTGTTCACTGGCCCCTCCCCCCCTTCCCCCCCCCCTGTATCTGTCCCTCTCCTCTCCCCTCCTGAAAAAAAGTCCTTTTCCCCCCTCTCTCCTGCCCCCCCCCCCCCCCCACTCCCCCCCCCCTCACCTTCCCCCTCTTCCCCTCCCCTCCTCCCCCTTCCCCCCTCCCTCCTCTCCCCTCCCCTCCCCCCTCCCCCCCTGCCTCCTCCCTTTCCCCCCCTTGTCCCCCCCCCCCCTCCTCTCTTTCCCCCTCCCTCCCCCCACCCTGCTCTGCCCCTTCCCCCTTCTTACCCCCCCCCCCCCCCTCCCTCTTCTGCCCCTTATGCCCATCCCCCTGTTCCCCCTTCCACGCCCTCCCCCCTGCCCCCCCCCTCCCCCCCCCCCCTGTCTCTGCCCTCCTCTTCCTCCCTCTGCCCATCTTTCTGCTTCCTAGTCCTGTATGCCCCTTTTCCTAACACTCACAACCAAAAACTAACTAATACTAAACATCTCAGACGCTCTGGAAATAGAAAACCGTTCTGAACTATCCTCGCCCGCCTTTCATTCTAGTCCTCATAGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGGAGGTCACGTTCCCTCCATTACCATCTTAAATCAAATTTGGCCACCAATGGTACTGAACTACGAGTTCCACCGACTACGGCGGACCAATCTTCAACTCCCAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAGTACTCTGCGTTGATACCAACTGCTTATGAGTGGCTTCGAGGGA 8&-*979@2?279-';>.5.65&57:772%5:-$?070$636&76976:7>562$792,176);/#*46;'6=59:99??-%2?17:799778&377>56:8$*6::7>56:776::6=5???,:9:79::6>56966<50%69@1<>160%63$07:2(17::$:77.?4:78;>=/5,%%36%-%4&%$(&9$%&+%(03:9%;($(/%$('&%%$7'%($#'#$$)%$$'#'$($51%#'$$%###$6#2*&##""#5%&/)%%$%%$$%&$$'/'&-*&8%&75&)655#&&%-453#02&-%#,2'%5:$&48($$$&($#%484#7%$.%*$-$%##)$*#->(:???,<59=?/,,,,,,#+(+(+...%(),.'*))),.-----$*(+...%+(),..&+(+.')+,,,,,,,,#*.....$)*++,,,,,,,,#+...%)$/&+)*(+.&*+,,&*...%+..&+.&),.....$+...%)))((+(+.&+(+(*.-----$+...%(+(*,,&*..&*.....$-()(....%+.&))(.&)(....%))(+.&+)+))*)(+...%+..&*.&+....%+))+...%*,-------------#$(+....%-(+(+.&+....%+..&)(,..&*...%*)*(+.&#*,,,,,,,,,#))(.&-)*(+.&+...%+.&+()**(.'*(+....%*))),..&+(%(+(+()(.&+.&)(.',(*..&+....%(*.....$+(+...%+.&)(.&),+,,,,,,,,,,#),(+),)(+)*(+.&)*++,,,,,,,,#+.&+,,,,,,,,,,,#*...%()))))&-..%*+,,,,,,,,,,,,,,,,#+(+.&+....%*+,,,,,,,,,##()(....%+.&+.&)++')))))($&.&)(..&)*+(+...%+(++,,,,,,,#+...%)%+(..&+,(+(+(+....%$..&)(.&))(+.&+(++,,,,,,,#*....%+..&+.&+..&+(+.&+..&+)+...%+.&&$$.&+...%$..&+.&)**))*()+*...%*.-----$((+,,,,,,,,#)*+)+()*+..&+(+.&+(+...%+.&),++++++$*+.&&$(#-....$$(+(+.&),,-------------,#)(++,,,,,,,,#+)#.&)(....%+()(...%+...%+.&$....%)(.....$+..&+.&+(+...%+...%*.....$*.-----$),.&+.&+..&))'------$)(*+,,,,,,,,,,,#+.&+(+())(....%+..&*.....$*..&),(+(),...%)(....%))()(*,------------,#+..&+())(),...%)()),..&)*....%)**(....%)(.'*(,..&*.....$),+,,,,,,,#*,,,,,,,,,,,#)*#(+(),..&+.&+()(.&+..&+(),..&)+())((),()(.&+)*+.&)*+)),...%)))(.&+,))*(+)*),).'),,+%(+,)(+,(*+(*,,'))+(+)),*(-(+()+(+,&*),+,,&.&**((),,((+)+.&+(,..&-.&))())*)(+)%,.&+))*),..&+..&)+..&++(-))+.&))(+))*,))),*(+)),)+)*(**(..&+.'))(*.')+()(,,&*)+,&))'+*.'*.',(),)++(),,((++(,)**(.'*.&,*(++(+*(+)*.',(+())),)(+..%&***********************#(*++++++$*++(+()-(**(,)*+.',)(),()()),)*)+*())(,)++(+ XQ:Z:30/32,44/46,0/0,0/0,26/26,0/0,46/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,57/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,46/46,0/0,0/0,23/26,0/0,58/60,45/50,30/32,43/46,0/0,0/0,26/26,0/0,48/60,46/50,30/32,44/46,0/0,0/0,23/26,0/0,58/60,45/50,30/32,42/46,0/0,0/0,26/26,0/0,52/60,44/50,27/32,40/46,0/0,0/0,26/26,0/0,58/60,50/50,28/32,43/46,0/0,0/0,26/26,0/0,56/60,38/50,30/32,41/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,38/50,21/32,46/46,0/0,0/0,24/26,0/0,58/60,45/50,22/32,38/46,0/0,0/0,24/26,0/0,58/60,38/50,23/32,43/46,0/0,0/0,26/26,0/0,56/60,45/50,22/32 SG:Z:O:0-16,VENUS:17-41,CBC:42-57,UMI:58-67,BOREAS:68-81,cDNA:82-1737,Poly_A:1738-1768,MARS:1769-1794,P:1795-1812 +read_fwd_10 0 chr1 632757 1 80S9=1X12=2X4=1I6=1X8=2D19=1D1=1X3=1X15=1I9=1X1=1X13=1D7=1X33=1I9=1X40=1028I1X1=1X2=2X4=2D1X1=1D3=2D1X1=2D15=1X32=1D5=1D14=1X7=1X7=1I4=1D8=1X10=1I5=1D6=1X12=1I7=1D23=1X3=1X13=2D2=1I2=1X2=1D10=1D2=2X5=2X1=1X13=1I19=1D1=1X11=1I25=1D10=2X5=1I2=1I11=1I7=1X11=1D12=1D1=1X6=1X20=2I6=1X8=1I5=1X8=1X17=1I12=1X4=2X23=67S * 0 0 AACCCCGGACACACTTAGTCTACACACCTCTTCCGAACTGCAACTAGGTGCAGACAGAGATCTCTCTTATCTTATATGGGATGGCACATTCAGCGCAAGTAGTCCTACAAAGACGGTACTTCCCATCATAGAAGAGCTTATCACCTTCTTGATCACGCCCTCATAAATCATTTTTCCTATCTGCTTCCTATCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAAATACTAACCTCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCCAACAACGTAAAACGCCACGGGCCGCACTAAGCACCACGCAACCTAACCCACTCCCGCTGATGGCAAGACGATCTCCAACCCAGACTGTATCCACCGACAAAAAATACGAAACCCGCCGGTCATACAACTCAATGTCCCCCAAACCCCTTCCCAAACGCACCTTCGTCCAACCCGAGCCACCTACCTCCTCCAGAAATGGCTACGCACTTCTACAACTGCTCTCGGCCCACAAATCTCCCCACTCAAGCTACGCGAACTTCTCGAACTAGCCACATACTCCCTCCTGGCACACCCACGACAAGCCACTGCACACTCACATAACAAACCCAACCCACCACCGGCATACACAGGCATACAACCAAGCCCCCACGGATCGCATCCAGCAAAACCCGCGACATGAGCCTTCCGGCCCAGGGCACACGCATCCAGACGACCGCTACCTGAAGCAGCCCAACCACGCCCTGAGCTCCCTCCGCACCGTGACATATCATACGAGCGGGCCCCCTAGATAGAGGTGCCCACCCTCCAAGACAAATAAAATACCATCATACTGAAAAGAACCCACCCGTAACTACAACAGTCACCCCTCAACCCGGCCCCAAAACCACACAAGTCCATCGGAACAGACCACCCCAAACACCCTCCCCCACTAAACCCCCTACAAACGAGCCCCAAACAAACCCACGTGAAGAATCCGACCCAGTACCCGCCCCCCCAAGCCACGCCCACGTCCCTACACTAAGTATTACCCCCCACCGCCGTCACACAGACCGACTTACCTCAAACCGATGTGCCCACCGTTTAGCACCGCCTCCCCCAGCCGACAAAGGGGTCAGGAGATCCTAGTCCTCATTGGGGGAGTAAACGAGCGCCAAAAACCCCTTACGAGAAATGTGGGACAAGCTGAGTATGTCAGCAACCTCCATCATATTAGACACATACACCCCGGTTAGGAAAAGAAGGACCGAGGTACTAGGAGTTCTCCAGCAGGTCCGATATACCTACAGGACCAACGCAACACGAAATCAGTGTCGAGCCCTCCCATCCCTAAGCATCCTTTACATAACAGACGAGGTCAACGATCCTCCTTACCATCAAATCACTTGGCCACCAATGGTAACTGACCTACGAGTACACCGACTAACGGCGACTAACCTTCAACTCCTATCATACTTCCCCATTATTCCTAGAACCAGGCAACCGGCGACTCCTTGACTGAACCATGAGTAGTACTCCTATTGAAAGCACCATTCGTATAATAAATTACATCACAAGACGTCTGCACTCATGAGCTTGTCCCCACATTAGGCTTAAAAACAATGCAATTCCTCGACGTCCTAAAACCAAACCATCTTTCACCGCTACACGACCGGGGTATACTACGTCAATGCACTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATACGTCCAAGAATTAAATCCCCTAAAAATCTTTGAAAATAGGGCCCGGATTTTACCTATAGCACCCCCTCTACCCCCCTCCTAGAAAGCCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTACTCTGCTTTGATCCCACAGCT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,7/26,0/0,56/60,43/50,30/32,39/46,0/0,0/0,26/26,0/0,56/60,38/50,26/32,32/46,0/0,0/0,23/26,0/0,56/60,34/50,23/32,37/46,0/0,0/0,23/26,0/0,60/60,40/50,30/32,46/46,0/0,0/0,16/26,0/0,58/60,42/50,27/32,32/46,0/0,0/0,18/26,0/0,54/60,48/50,22/32,35/46,0/0,0/0,21/26,0/0,60/60,39/50,30/32,37/46,0/0,0/0,22/26,0/0,60/60,42/50,23/32,39/46,0/0,0/0,16/26,0/0,60/60,39/50,17/32,43/46,0/0,0/0,26/26,0/0 SG:Z:E:0-17,VENUS:18-39,CBC:40-55,UMI:56-65,BOREAS:66-80,cDNA:81-1810,Poly_A:1811-1840,MARS:1841-1864 diff --git a/tests/test_data/tagfix/tagfix_test_data.sam b/tests/test_data/tagfix/tagfix_test_data.sam new file mode 100644 index 00000000..0f03eb14 --- /dev/null +++ b/tests/test_data/tagfix/tagfix_test_data.sam @@ -0,0 +1,221 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 +@SQ SN:chr2 LN:242193529 +@SQ SN:chr3 LN:198295559 +@SQ SN:chr4 LN:190214555 +@SQ SN:chr5 LN:181538259 +@SQ SN:chr6 LN:170805979 +@SQ SN:chr7 LN:159345973 +@SQ SN:chr8 LN:145138636 +@SQ SN:chr9 LN:138394717 +@SQ SN:chr10 LN:133797422 +@SQ SN:chr11 LN:135086622 +@SQ SN:chr12 LN:133275309 +@SQ SN:chr13 LN:114364328 +@SQ SN:chr14 LN:107043718 +@SQ SN:chr15 LN:101991189 +@SQ SN:chr16 LN:90338345 +@SQ SN:chr17 LN:83257441 +@SQ SN:chr18 LN:80373285 +@SQ SN:chr19 LN:58617616 +@SQ SN:chr20 LN:64444167 +@SQ SN:chr21 LN:46709983 +@SQ SN:chr22 LN:50818468 +@SQ SN:chrX LN:156040895 +@SQ SN:chrY LN:57227415 +@SQ SN:chrM LN:16569 +@SQ SN:chr1_KI270706v1_random LN:175055 +@SQ SN:chr1_KI270707v1_random LN:32032 +@SQ SN:chr1_KI270708v1_random LN:127682 +@SQ SN:chr1_KI270709v1_random LN:66860 +@SQ SN:chr1_KI270710v1_random LN:40176 +@SQ SN:chr1_KI270711v1_random LN:42210 +@SQ SN:chr1_KI270712v1_random LN:176043 +@SQ SN:chr1_KI270713v1_random LN:40745 +@SQ SN:chr1_KI270714v1_random LN:41717 +@SQ SN:chr2_KI270715v1_random LN:161471 +@SQ SN:chr2_KI270716v1_random LN:153799 +@SQ SN:chr3_GL000221v1_random LN:155397 +@SQ SN:chr4_GL000008v2_random LN:209709 +@SQ SN:chr5_GL000208v1_random LN:92689 +@SQ SN:chr9_KI270717v1_random LN:40062 +@SQ SN:chr9_KI270718v1_random LN:38054 +@SQ SN:chr9_KI270719v1_random LN:176845 +@SQ SN:chr9_KI270720v1_random LN:39050 +@SQ SN:chr11_KI270721v1_random LN:100316 +@SQ SN:chr14_GL000009v2_random LN:201709 +@SQ SN:chr14_GL000225v1_random LN:211173 +@SQ SN:chr14_KI270722v1_random LN:194050 +@SQ SN:chr14_GL000194v1_random LN:191469 +@SQ SN:chr14_KI270723v1_random LN:38115 +@SQ SN:chr14_KI270724v1_random LN:39555 +@SQ SN:chr14_KI270725v1_random LN:172810 +@SQ SN:chr14_KI270726v1_random LN:43739 +@SQ SN:chr15_KI270727v1_random LN:448248 +@SQ SN:chr16_KI270728v1_random LN:1872759 +@SQ SN:chr17_GL000205v2_random LN:185591 +@SQ SN:chr17_KI270729v1_random LN:280839 +@SQ SN:chr17_KI270730v1_random LN:112551 +@SQ SN:chr22_KI270731v1_random LN:150754 +@SQ SN:chr22_KI270732v1_random LN:41543 +@SQ SN:chr22_KI270733v1_random LN:179772 +@SQ SN:chr22_KI270734v1_random LN:165050 +@SQ SN:chr22_KI270735v1_random LN:42811 +@SQ SN:chr22_KI270736v1_random LN:181920 +@SQ SN:chr22_KI270737v1_random LN:103838 +@SQ SN:chr22_KI270738v1_random LN:99375 +@SQ SN:chr22_KI270739v1_random LN:73985 +@SQ SN:chrY_KI270740v1_random LN:37240 +@SQ SN:chrUn_KI270302v1 LN:2274 +@SQ SN:chrUn_KI270304v1 LN:2165 +@SQ SN:chrUn_KI270303v1 LN:1942 +@SQ SN:chrUn_KI270305v1 LN:1472 +@SQ SN:chrUn_KI270322v1 LN:21476 +@SQ SN:chrUn_KI270320v1 LN:4416 +@SQ SN:chrUn_KI270310v1 LN:1201 +@SQ SN:chrUn_KI270316v1 LN:1444 +@SQ SN:chrUn_KI270315v1 LN:2276 +@SQ SN:chrUn_KI270312v1 LN:998 +@SQ SN:chrUn_KI270311v1 LN:12399 +@SQ SN:chrUn_KI270317v1 LN:37690 +@SQ SN:chrUn_KI270412v1 LN:1179 +@SQ SN:chrUn_KI270411v1 LN:2646 +@SQ SN:chrUn_KI270414v1 LN:2489 +@SQ SN:chrUn_KI270419v1 LN:1029 +@SQ SN:chrUn_KI270418v1 LN:2145 +@SQ SN:chrUn_KI270420v1 LN:2321 +@SQ SN:chrUn_KI270424v1 LN:2140 +@SQ SN:chrUn_KI270417v1 LN:2043 +@SQ SN:chrUn_KI270422v1 LN:1445 +@SQ SN:chrUn_KI270423v1 LN:981 +@SQ SN:chrUn_KI270425v1 LN:1884 +@SQ SN:chrUn_KI270429v1 LN:1361 +@SQ SN:chrUn_KI270442v1 LN:392061 +@SQ SN:chrUn_KI270466v1 LN:1233 +@SQ SN:chrUn_KI270465v1 LN:1774 +@SQ SN:chrUn_KI270467v1 LN:3920 +@SQ SN:chrUn_KI270435v1 LN:92983 +@SQ SN:chrUn_KI270438v1 LN:112505 +@SQ SN:chrUn_KI270468v1 LN:4055 +@SQ SN:chrUn_KI270510v1 LN:2415 +@SQ SN:chrUn_KI270509v1 LN:2318 +@SQ SN:chrUn_KI270518v1 LN:2186 +@SQ SN:chrUn_KI270508v1 LN:1951 +@SQ SN:chrUn_KI270516v1 LN:1300 +@SQ SN:chrUn_KI270512v1 LN:22689 +@SQ SN:chrUn_KI270519v1 LN:138126 +@SQ SN:chrUn_KI270522v1 LN:5674 +@SQ SN:chrUn_KI270511v1 LN:8127 +@SQ SN:chrUn_KI270515v1 LN:6361 +@SQ SN:chrUn_KI270507v1 LN:5353 +@SQ SN:chrUn_KI270517v1 LN:3253 +@SQ SN:chrUn_KI270529v1 LN:1899 +@SQ SN:chrUn_KI270528v1 LN:2983 +@SQ SN:chrUn_KI270530v1 LN:2168 +@SQ SN:chrUn_KI270539v1 LN:993 +@SQ SN:chrUn_KI270538v1 LN:91309 +@SQ SN:chrUn_KI270544v1 LN:1202 +@SQ SN:chrUn_KI270548v1 LN:1599 +@SQ SN:chrUn_KI270583v1 LN:1400 +@SQ SN:chrUn_KI270587v1 LN:2969 +@SQ SN:chrUn_KI270580v1 LN:1553 +@SQ SN:chrUn_KI270581v1 LN:7046 +@SQ SN:chrUn_KI270579v1 LN:31033 +@SQ SN:chrUn_KI270589v1 LN:44474 +@SQ SN:chrUn_KI270590v1 LN:4685 +@SQ SN:chrUn_KI270584v1 LN:4513 +@SQ SN:chrUn_KI270582v1 LN:6504 +@SQ SN:chrUn_KI270588v1 LN:6158 +@SQ SN:chrUn_KI270593v1 LN:3041 +@SQ SN:chrUn_KI270591v1 LN:5796 +@SQ SN:chrUn_KI270330v1 LN:1652 +@SQ SN:chrUn_KI270329v1 LN:1040 +@SQ SN:chrUn_KI270334v1 LN:1368 +@SQ SN:chrUn_KI270333v1 LN:2699 +@SQ SN:chrUn_KI270335v1 LN:1048 +@SQ SN:chrUn_KI270338v1 LN:1428 +@SQ SN:chrUn_KI270340v1 LN:1428 +@SQ SN:chrUn_KI270336v1 LN:1026 +@SQ SN:chrUn_KI270337v1 LN:1121 +@SQ SN:chrUn_KI270363v1 LN:1803 +@SQ SN:chrUn_KI270364v1 LN:2855 +@SQ SN:chrUn_KI270362v1 LN:3530 +@SQ SN:chrUn_KI270366v1 LN:8320 +@SQ SN:chrUn_KI270378v1 LN:1048 +@SQ SN:chrUn_KI270379v1 LN:1045 +@SQ SN:chrUn_KI270389v1 LN:1298 +@SQ SN:chrUn_KI270390v1 LN:2387 +@SQ SN:chrUn_KI270387v1 LN:1537 +@SQ SN:chrUn_KI270395v1 LN:1143 +@SQ SN:chrUn_KI270396v1 LN:1880 +@SQ SN:chrUn_KI270388v1 LN:1216 +@SQ SN:chrUn_KI270394v1 LN:970 +@SQ SN:chrUn_KI270386v1 LN:1788 +@SQ SN:chrUn_KI270391v1 LN:1484 +@SQ SN:chrUn_KI270383v1 LN:1750 +@SQ SN:chrUn_KI270393v1 LN:1308 +@SQ SN:chrUn_KI270384v1 LN:1658 +@SQ SN:chrUn_KI270392v1 LN:971 +@SQ SN:chrUn_KI270381v1 LN:1930 +@SQ SN:chrUn_KI270385v1 LN:990 +@SQ SN:chrUn_KI270382v1 LN:4215 +@SQ SN:chrUn_KI270376v1 LN:1136 +@SQ SN:chrUn_KI270374v1 LN:2656 +@SQ SN:chrUn_KI270372v1 LN:1650 +@SQ SN:chrUn_KI270373v1 LN:1451 +@SQ SN:chrUn_KI270375v1 LN:2378 +@SQ SN:chrUn_KI270371v1 LN:2805 +@SQ SN:chrUn_KI270448v1 LN:7992 +@SQ SN:chrUn_KI270521v1 LN:7642 +@SQ SN:chrUn_GL000195v1 LN:182896 +@SQ SN:chrUn_GL000219v1 LN:179198 +@SQ SN:chrUn_GL000220v1 LN:161802 +@SQ SN:chrUn_GL000224v1 LN:179693 +@SQ SN:chrUn_KI270741v1 LN:157432 +@SQ SN:chrUn_GL000226v1 LN:15008 +@SQ SN:chrUn_GL000213v1 LN:164239 +@SQ SN:chrUn_KI270743v1 LN:210658 +@SQ SN:chrUn_KI270744v1 LN:168472 +@SQ SN:chrUn_KI270745v1 LN:41891 +@SQ SN:chrUn_KI270746v1 LN:66486 +@SQ SN:chrUn_KI270747v1 LN:198735 +@SQ SN:chrUn_KI270748v1 LN:93321 +@SQ SN:chrUn_KI270749v1 LN:158759 +@SQ SN:chrUn_KI270750v1 LN:148850 +@SQ SN:chrUn_KI270751v1 LN:150742 +@SQ SN:chrUn_KI270752v1 LN:27745 +@SQ SN:chrUn_KI270753v1 LN:62944 +@SQ SN:chrUn_KI270754v1 LN:40191 +@SQ SN:chrUn_KI270755v1 LN:36723 +@SQ SN:chrUn_KI270756v1 LN:79590 +@SQ SN:chrUn_KI270757v1 LN:71251 +@SQ SN:chrUn_GL000214v1 LN:137718 +@SQ SN:chrUn_KI270742v1 LN:186739 +@SQ SN:chrUn_GL000216v2 LN:176608 +@SQ SN:chrUn_GL000218v1 LN:161147 +@SQ SN:chrEBV LN:171823 +@PG PN:minimap2 ID:minimap2 VN:2.24-r1122 CL:minimap2 -ayYL --MD --eqx -x splice:hq -t 4 /cromwell_root/broad-dsde-methods-long-reads/resources/references/grch38_noalt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa tmp.fastq +@PG PN:restore-annotations ID:restore-annotations-0.0.1 VN:0.0.1 DS:Reads an unaligned bam with annotations and an aligned bam containing the same reads. Copies tags on the unaligned bam to reads in the aligned file with the same name. CL:/lrma/restore_annotations_to_aligned_bam.py --bam shard.bam --aligned-bam out.bam --out-name out.AnnotationsRestored.bam +@PG ID:GATK PrintReads VN:4.2.4.1-1-gcaa48f9 CL:PrintReads --output out.bam --input aligned.bam --read-filter MappedReadFilter --read-filter MappingQualityNotZeroReadFilter --read-filter NotSecondaryAlignmentReadFilter --read-filter NotSupplementaryAlignmentReadFilter --read-filter ReadLengthReadFilter --read-filter ExcessiveEndClippedReadFilter --disable-read-filter WellformedReadFilter --max-read-length 15000 --max-clipped-bases 1000 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --min-read-length 1 PN:GATK PrintReads +@PG PN:longbow ID:longbow-pad-0.5.27 VN:0.5.27 DS:Pad tag by specified number of adjacent bases from the read. MODEL(s): {"name": "mas15v2", "description": "The standard MAS-seq 15 array element model.", "version": "2.0.0", "array_element_structure": [["A", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["B", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["C", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["D", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["E", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["F", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["G", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["H", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["I", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["J", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["K", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["L", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["M", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["N", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["O", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS", "P"]], "adapters": {"VENUS": "TCTACACGACGCTCTTCCGATCT", "Poly_A": {"HomopolymerRepeat": ["A", 30]}, "MARS": "GTACTCTGCGTTGATACCACTGCTT", "BOREAS": "TTTCTTATATGGG", "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", "D": "ACCTCCTCCTCCAGAA", "E": "AACCGGACACACTTAG", "F": "AGAGTCCAATTCGCAG", "G": "AATCAAGGCTTAACGG", "H": "ATGTTGAATCCTAGCG", "I": "AGTGCGTTGCGAATTG", "J": "AATTGCGTAGTTGGCC", "K": "ACACTTGGTCGCAATC", "L": "AGTAAGCCTTCGTGTC", "M": "ACCTAGATCAGAGCCT", "N": "AGGTATGCCGGTTAAG", "O": "AAGTCACCGGCACCTT", "P": "ATGAAGTGGCTCGAGA", "CBC": {"FixedLengthRandomBases": 16}, "UMI": {"FixedLengthRandomBases": 10}, "cDNA": "random"}, "direct_connections": {"Poly_A": ["MARS"], "MARS": ["K", "P", "D", "G", "J", "E", "A", "F", "N", "O", "M", "C", "H", "I", "B", "L"], "A": ["VENUS"], "B": ["VENUS"], "C": ["VENUS"], "D": ["VENUS"], "E": ["VENUS"], "F": ["VENUS"], "G": ["VENUS"], "H": ["VENUS"], "I": ["VENUS"], "J": ["VENUS"], "K": ["VENUS"], "L": ["VENUS"], "M": ["VENUS"], "N": ["VENUS"], "O": ["VENUS"], "P": ["VENUS"], "VENUS": ["CBC"], "CBC": ["UMI"], "UMI": ["BOREAS"], "BOREAS": ["cDNA"], "cDNA": ["Poly_A"]}, "start_element_names": ["A", "VENUS"], "end_element_names": ["P", "Poly_A"], "named_random_segments": ["UMI", "CBC", "cDNA"], "coding_region": "cDNA", "annotation_segments": {"UMI": [["ZU", "XU"], ["XM", "XU"]], "CBC": [["CR", "XB"], ["XC", "XB"]]}} CL:/longbow/venv/bin/longbow pad --model mas15v2 -v INFO --barcode-tag CR -e 2 -o tmp.bam -n CR shard_0.bam +@PG PN:longbow ID:longbow-correct-0.5.28 VN:0.5.28 DS:Correct tag to values provided in barcode allowlist. MODEL(s): {"name": "mas15v2", "description": "The standard MAS-seq 15 array element model.", "version": "2.0.0", "array_element_structure": [["A", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["B", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["C", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["D", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["E", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["F", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["G", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["H", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["I", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["J", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["K", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["L", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["M", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["N", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS"], ["O", "VENUS", "CBC", "UMI", "BOREAS", "cDNA", "Poly_A", "MARS", "P"]], "adapters": {"VENUS": "TCTACACGACGCTCTTCCGATCT", "Poly_A": {"HomopolymerRepeat": ["A", 30]}, "MARS": "GTACTCTGCGTTGATACCACTGCTT", "BOREAS": "TTTCTTATATGGG", "A": "AGCTTACTTGTGAAGA", "B": "ACTTGTAAGCTGTCTA", "C": "ACTCTGTCAGGTCCGA", "D": "ACCTCCTCCTCCAGAA", "E": "AACCGGACACACTTAG", "F": "AGAGTCCAATTCGCAG", "G": "AATCAAGGCTTAACGG", "H": "ATGTTGAATCCTAGCG", "I": "AGTGCGTTGCGAATTG", "J": "AATTGCGTAGTTGGCC", "K": "ACACTTGGTCGCAATC", "L": "AGTAAGCCTTCGTGTC", "M": "ACCTAGATCAGAGCCT", "N": "AGGTATGCCGGTTAAG", "O": "AAGTCACCGGCACCTT", "P": "ATGAAGTGGCTCGAGA", "CBC": {"FixedLengthRandomBases": 16}, "UMI": {"FixedLengthRandomBases": 10}, "cDNA": "random"}, "direct_connections": {"Poly_A": ["MARS"], "MARS": ["J", "N", "A", "F", "G", "H", "L", "O", "B", "P", "I", "E", "K", "C", "M", "D"], "A": ["VENUS"], "B": ["VENUS"], "C": ["VENUS"], "D": ["VENUS"], "E": ["VENUS"], "F": ["VENUS"], "G": ["VENUS"], "H": ["VENUS"], "I": ["VENUS"], "J": ["VENUS"], "K": ["VENUS"], "L": ["VENUS"], "M": ["VENUS"], "N": ["VENUS"], "O": ["VENUS"], "P": ["VENUS"], "VENUS": ["CBC"], "CBC": ["UMI"], "UMI": ["BOREAS"], "BOREAS": ["cDNA"], "cDNA": ["Poly_A"]}, "start_element_names": ["VENUS", "A"], "end_element_names": ["Poly_A", "P"], "named_random_segments": ["CBC", "cDNA", "UMI"], "coding_region": "cDNA", "annotation_segments": {"UMI": [["ZU", "XU"], ["XM", "XU"]], "CBC": [["CR", "XB"], ["XC", "XB"]]}} CL:/longbow/venv/bin/longbow correct -t 1 --model mas15v2 --allow-list short_read_barcodes_no_counts.txt -v INFO --barcode-tag CR --corrected-tag CB --max-hifi-dist 2 --max-clr-dist 2 -o shard_0_corrected_barcodes.bam --barcode-uncorrectable-bam shard_0_uncorrected_barcodes.bam shard_0.bam +read_rev_1 16 chr1 14362 5 120S102=1X365=140N69=757N24=1X70=78S * 0 0 ATCTCGAGCCACTTCATAAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACTGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTTCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACCCCATATAAGAAAGCCCTTCAGTATCTTGGGACCGGTGTAGATCGGAAGAGCGTCGTGTAGAAAGGTGCCGGTGACTT ~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+~~~~~~~~~~~~~~~~~~~~~j~~~~~~S~~~~~~~~~~~x~~{~~~~~~~~~r~~~U~~~~~~~~r~x~~~w~~~~dh~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~p~~~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~J~~~~S~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~~~~~~t~~j~~~m~~~~~~~~~~y~~~~~~~~|~~~~~~~~x~~~~~~~~x~x~~~~~~~I~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~W~~~~~w~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~p~~~s~~~~~~~~~~~~~~l~~~}~~~~~~~~|~~x~~~{~~~~~~~~~~k~~~~~~~~x~~w~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~j~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~y~p~~~~~~~~~~~~ XQ:Z:42/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,50/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,54/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,52/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,52/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,44/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,32/32 SG:Z:O:0-15,VENUS:16-38,CBC:39-54,UMI:55-64,BOREAS:65-78,cDNA:79-708,Poly_A:709-787,MARS:788-812,P:813-829 +read_rev_2 16 chr1 14366 40 173S6=1I13=1I16=1I21=1X6=1I3=1D4=1D12=1D3=1X9=1X23=2D7=1D29=2X3=1I16=1D7=1X5=1I16=1I8=2I14=1D23=1D9=1D8=1D15=1I8=2X18=1I19=1X2=1X8=1D9=1D7=1I6=1I38=1D13=1X8=1I10=1I5=1X10=1D140N11=1X12=1X3=2I5=1I5=1I5=1I23=1D5=1I35=1X13=2X3=1X18=1X5=1D5=1I58=1X14=1D12=1D6=1X1=1I11=1D25=77S * 0 0 AAGCAGTGTATCAACGCAGAAGTACTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTGTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTATTTTTTTTATTTTTTTTATTTTTTTATTATTTTATTTTTTTTCCGCACAGTCTAGAGATCCTTTAATTAAAAGCACACTGTATGGTTTCTGCTCAGTTCTTTAATGATTGTGTGGCCGTTTCTCTGGAAGCTCATAAGAACACTGTGGCGCAGGCTGGGTGGAGCCGCCCCCATGAGCACAGGCAGACAGAAGTCCCCGCCCCCACTGTTGTGGCCTCAAGCCAGCTTCCGCACCTTGAAAGCTGGTCTCCACACAAGTGCTGGTTTTCCGTCACCCCCTCCAAGGAAGTAGGTCTGAGCAGCTGTCCTGGCGTGTCCATTCAGAGCAACGGCCCGAAGTCTGGTCCTGGGGGGGAAGGTGTCATTGGAGCCCCCTACGATTCCAAGACGTCCTCGCCTCCTCTGCTGTGGCATGCTGCGGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAGGCTCCTCCGGACCCCTCACACAGCCCCAGGTTCCTTACCCAGAGATGCCTTGCGCCTCGTGACCAGCTTGTAGAAGTGAGATCCCGACAATCAACGTGCCCACCTTGGCTCGTGGCTCCACTGCCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCATTCACATGCGACCGTGGACACCCTGTCCCCACCCCCATTACACTCCCAGACCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAACACCGGGCACTGATAGACAGCGGCTGTTGAGGCGCCCACCTCCCAGCACCTCGGGGCCAGGGCCAGGGTGTCCCCAAATAAGAAACACGCGGCTTGCTTGGTGAATGTAGAGACCGAAGAGCGTCCGTGTAGAGCCAACTACGCACTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:22/32,38/46,0/0,0/0,26/26,0/0,54/60,35/50,27/32,43/46,0/0,0/0,24/26,0/0,52/60,38/50,32/32,44/46,0/0,0/0,26/26,0/0,55/60,42/50,20/32,42/46,0/0,0/0,26/26,0/0,52/60,38/50,30/32,41/46,0/0,0/0,21/26,0/0,50/60,43/50,24/32,40/46,0/0,0/0,26/26,0/0,56/60,43/50,22/32,42/46,0/0,0/0,26/26,0/0,54/60,38/50,30/32,37/46,0/0,0/0,22/26,0/0,30/60,42/50,27/32,34/46,0/0,0/0,26/26,0/0,50/60,38/50,24/32,31/46,0/0,0/0,22/26,0/0,60/60,40/50,25/32,42/46,0/0,0/0,26/26,0/0,46/60,43/50,26/32,38/46,0/0,0/0,23/26,0/0 SG:Z:J:0-14,VENUS:15-36,CBC:37-52,UMI:53-62,BOREAS:63-76,cDNA:77-834,Poly_A:835-980,MARS:981-1005 +read_rev_3 16 chr1 14368 41 80S14=1I4=1I16=1I7=2I1X11=2X2=2X5=2I14=2I29=1I1=3I11=1X2=7I17=1D24=1I4=1X4=1I5=1I3=2I9=1I3=1D12=2X11=1X5=1I8=1I1=1I2=1X3=2I6=1I8=3I1=1I7=1D11=1X28=5I3=4I8=1I3=1D1=1D4=1D14=1I9=1X2=1I16=1I5=1I2=2I5=1D3=1I3=1I3=8I7=3I2=2I11=4I6=1X12=1X2=2I2=1I3=1X7=1I1=1I17=140N5=1I37=1I17=1I10=757N3=2I3=1D7=1X1=1X3=1D1=1D1=1X1=1D7=1I3=4I2=1D2=1D15=1I6=2X6=1I13=1I11=1D1X2=1D1=1X2=1I3=2I1=1I5=2X5=2I2=3I4=1X12=1I12=659N7=3I10=1I6=1I4=1D1=1X5=7I7=2X3=1D9=1X3=2I5=1X7=15I1=1I7=6I15=1I6=1D6=1I4=1I1=2I1=2I9=18I5=1I8=11I2=1X1=1D1=1X9=1I2=1X1=1X92N9=1I9=1I15=2I8=1X3=2X4=2I13=5I4=1I7=8I3=4I18=1I5=1I2=1I10=2I3=1I1X8=1I5=1D32=1I11=2X1=1X20=177N3=1X2=1I10=1I5=2I5=2D4=1I9=1D12=1X9=1I2=1I7=1D3=2I5=1X7=1X2=2I1=1I2=1I8=1I2=1X8=1I3=1I3=6I7=2I3=1X4=237N1X7=1D4=1I4=1X15=1I2=2I3=1D4=2I17=1D3=1X7=1X6=2X17=1I4=7I3=1I6=1X2=3X4=1X1=1I7=2X5=172N15=1I1X1=3I8=1X3=1I2=1I9=1X9=3I5=4I7=1I10=2I10=1I4=1I9=21I4=1X6=1X16=1X1=5I4=1D2=1D10=2I1=1D2=206N6=1D5=2I1=1X13=1D7=3I1X35=1I2=1I6=1X2=1I8=332S * 0 0 AAGCGAGTGGTGTATCAACGCAGAGTACATTTTTTTTTTTTTTTCTTTTTTTATTTTTTTTTTGTTTTTTTACTTGCACTACAGCTAGAGATCCTTTTATTTAAAAGCACACTGTTGGGTTTCTCCCCTCAGTTCTTTTATGCATGGTGTTTGCCGTTTTCTCTGGAGAAGCCTCTTAAGAACACAGTGGCGCAGGACTTGTGGGTGGAGCCTTCCATCCCACCCCCATGGAGCACAGGAGACAGAAGTCCCCGCCCCAGCTGATGTGACCTCAAAGCCTAGCCTCTTCCGCTCACTTAAGCTGGTCTCCCAACAGTGCTGGTACCGTCAACCCCCTCACACATGGACCAGTAGGTTCTGAGCACACGTCTTGTCCGGCTGTGTCCAGGTCAGAGCAACGGCCCAAGTCTGGGTCTTGGGCGGGACATGGGGAAGGTTGTAGGAGCCCCTACGATTCCCTAGTCGTCCTTGTCCCTCCTCTGCCTGTGGCCTGCTGGCGTGGTGGGGCAAGACGGACGGTGGTTGGGATGGATAAGTCTCTGACACGCGGTCTGGCAAAAGCTCCTCCGGGCACCTATCTACCCGCCCCAGTGTTCCTTTCCCAGAGATGCCCTTGCCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCATAGTGCCCACCTTGGCTCTGTGGCTCTCACTTTGGCTCTGCTCCGTATGCGTTCTCTCCAGTCTTCTAGTCCTCTTCATGCTGCGCAGCCTTGGCTGTGCCGATTGCCCCCAGCTTGAGCGGATGGACTGAGAAAGTTGGACCACAGCCCTCGGAGGCGGATTGTCATCCACTTCCCTGGTGAGCTCCCTGGACTGAAGGGGTAGACGCGCTGCCTGCTGACTGTGGCCTGCCTGGCATCTGGCGCACTGGCTACAGGGGACGCTAGGTTGTGGGTGGGCGACGCTGTAGGAGCATGTGGGGGGTCTGTTGCACTGGCCAGCACACTCAGGGCTGGGCGGTGTGATTCCGGTGGGGGCGTCGGTACGGTCTGGGGTGGTGGTGGGTGGTGCGAGGGTGGTTTTTGAACCCATCTTGTTATGGCTTGAGAGGCCTCGGCTACACTCAGTGTGGAAGGTGGGGGCAGTTATGGTTTGGTTGGCCAGGGGCAGAGGCCGTGGGGCCAATGCCGTGGCAGGGGGCCCAGCCCAGGTCGGCAATGTACCATGACGGTTCGTTGGCAACTTGCAAGGGCAGGTACAGGCGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCCAGGTCTGGACCTTAGAAGTAGTTCTCTGGGACCTGTTGTTTCCAGCTGCTTCTCTGGCTTGCATGGAACAAGGGGGATCAAACAGCTTATCCTCTGTCTTCTTGCCCCCGCAACTCACAGGGGTCTTAGTAATGACAAGCACCAGCCCTGGGGGTCCAAGGAAAGAAAAAAACATACTTATCTCCTACTGGTTCTCGTGGTTGTTCAAGAGCAGCAAGGAGTCTAGGACGAGCCTTGATGTTGCTGGGAAGACCCAAAGTCCCGCTTCTGATTCGTCCTCGGGCTCCGGTCTTGCAAGTGCGTGCCTCACGAACCTCGGAATGCTCCTTCAAGTTCTCCTGCAGGGCCCGCTCAATACACCAGGGGGAGGTCGCTTTGCTCTGGGTCCTGTGGCCTAGGGGGCATCCGTCTCTCGCAGGCCAGGGCGTCCTGGGCGCCCCGTTGAAGATGGAAATACGAAGAATGAAATGGTAGCCTTATTCCAGCAGGCGCCCTGGAGCTGCGGGAGGTATTGCACTGGAGATTAACCTTGATGCCTTTCCGTGCTGCCCTTGATTTCTCAACCCCCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGACCGTGCACCGGGCCTCCGGCTTATCGCCTCTAACATGCTGAAGATGTCTGCAGGACCCTTCTATGCAGTACTGCAGGGCATTTTTCCGCCATCTGTGGTGGCCTACCTCTCGCGCAGGTCTGGACACCACCCCTGGATGAGGGGCTAGGCATAGGTCTGTACCTGCAAGGGGCTCATAGAGCTGCATCTACTACACAGGGAGTCATGGAGCCCCCCCCCCCCCCCCGGCTGCGGCCGCCTACCGGAAAGCTCCCCGCCGCACCCCATATATAGAAAATAGGGTGGGATCGACCGATGGTCTATAGATCGGAAATAATGAAGGAGCGGCGCTGTAGACGCTAGGATTCAACAAT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,8/26,0/0,51/60,36/50,28/32,28/46,0/0,0/0,23/26,0/0,54/60,41/50,27/32,25/46,0/0,0/0,23/26,0/0,56/60,29/50,25/32,46/46,0/0,0/0,15/26,0/0,60/60,35/50,30/32,38/46,0/0,0/0,17/26,0/0 SG:Z:H:0-16,VENUS:17-50,CBC:51-66,UMI:67-76,BOREAS:77-91,cDNA:92-2157,Poly_A:2158-2200,MARS:2201-2228 +read_rev_4 16 chr1 14398 1 50S5=1X2=1I16=1D1X12=1D1X18=5I4=1X3=1D20=1I6=1X25=1I12=1I3=1I1X9=1X2=2X4=2X5=1I13=3I3=1X9=1I13=1I2=2X3=1X5=1X5=2I1=1I1X5=1I12=1D3=1D13=1X5=3I13=1X9=1I1=1I4=1D18=1I2=1D12=1I2=1I12=2X20=1I11=1X14=1D8=1D10=2I2=1D7=1I4=2I1=1I4=2I5=1X2=140N2=1D5=4I6=1D5=1I13=1D7=1I4=1X23=171278N1=1X1=1D2=1I17=1X8=1I11=2I2=1I3=1X4=1I6=1X1=1X21=1I1X11=13I1=2I10=1D6=1I5=1D17=1I14=1D2=659N11=1D8=1I4=1D20=1D13=3I20=1I2=1X1=1X8=1I2=1I18=1X3=1D22=6I5=1I12=1D2=92N2=2I4=1X5=1D5=2I1=1X13=2D6=1I1=1X4=1D3=1I4=1I5=1I3=1D5=1D8=1I13=1X1=2I4=1D2=1I8=1D10=1D5=2I13=2X7=76S * 0 0 AAGCAGTGGTATCCACGGAGAGTACTTTTTTTTTTATTTTTTTTTATTTTTGTTGTTTCTCTGCTCAGTTCTTTAAGATTGGTGTGCCATTTCTCTGGAAGCCTCTTCAGAGAAGATCACGTGGCGCAGGCTGGGTGGAGTCCGTCCACCCATGGAGCACAGGCAGACAGAAGTTCCCCGCCCCAGACTGAAGTGGCCTCAGGCAGGCCTCTCGCTCGCTTGAAGCTGGTCTCATCCGCACAGTGCTGGGTTCCGTCACCCGCCAACCAGGGAAGCAGGTCCTTATAGCAGCCTTGTCCTGGCTTGTCATGTCAGAGCAATGGCCCAAGAAGTCTGGGTCTGTGGGGGAAGGATGGTCAGGAGCCCCCTACGATTCCGCATCGTCCTCGTCCTTCACTCTGCCTGTGGACGCTGCGGTGGCGGCAGAGGACGGGATGGAGTCGGACACGCGGGCAAAGCTCCTCCGGCCCCTCACAGCACCCCAGGATCCTAGTCTCCCCAAGAGAGGCCCTGCGCGGCGCTCATGCCAGCTTTGTTGAAGAGATCGACATCAAAGTCCCCACCTTGGCTCGTGGCTCTCACGTCTACCTGCTCCTTCTGCTTCGTCTTCTCCAAGCTTTCGCTCATCTATCACGCTGACGCAGCATTGCCTTGCCGATGCCCCCAGCTGGGGCGGATGGACCCCCTCCCCCACTTCCCTAGCAGAGTGCCCGGCCCACCGAGGGGTCGACCACTTCGCCTGGGAGCTCCCTGACTGAAGGAGACCGCTGCTGCCTGCGTCGTCCTGCCTGGCGCCTTGCCTACAGGGGCCCAAGCGGTTGAGGGTGGGAGTGGTGGATTCACTGGCCTAGCCACCTCAGGAGCTGGGGGAGGTGTGGGGGCGGTGGGGGTGGTGTGTGCTGTAGTACCCCCATCTTGTAGTCTGCTGAGTGGCTCGCTACCACACAGTGTGGAAGGTGCAGTTCCCGGAAGGTGGCCAGGGGGCAAGAGGGGCATGCCGGGTGCCCAGGTCGGCACTGAGTACTGTAGGTCGTTGCAATGCCGGCAGGTCACAGGCAGGTAGGACAGAACATCCCATATCGCAACACAAACGTAGATTGCATGGCTCACGAGAGCGAAAGAGCGTCGTGTAAGAACCGTAAGCGTGATT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:21/32,30/46,0/0,0/0,23/26,0/0,56/60,40/50,17/32,39/46,0/0,0/0,24/26,0/0,60/60,31/50,24/32,35/46,0/0,0/0,22/26,0/0,54/60,44/50,26/32,35/46,0/0,0/0,26/26,0/0,48/60,37/50,28/32,24/46,0/0,0/0,22/26,0/0,60/60,40/50,26/32,36/46,0/0,0/0,21/26,0/0,56/60,28/50,18/32,33/46,0/0,0/0,14/26,0/0,46/60,40/50,24/32,37/46,0/0,0/0,26/26,0/0,54/60,31/50,27/32,35/46,0/0,0/0,26/26,0/0,60/60,39/50,13/32,36/46,0/0,0/0,23/26,0/0,56/60,38/50,24/32,27/46,0/0,0/0,22/26,0/0,58/60,41/50,24/32,33/46,0/0,0/0,21/26,0/0 SG:Z:G:0-14,VENUS:15-38,CBC:39-54,UMI:55-64,BOREAS:65-77,cDNA:78-1091,Poly_A:1092-1124,MARS:1125-1149 +read_rev_5 16 chr1 14400 29 159S395=1I24=1D10=140N69=757N108=1I39=664N26=1I133=92N26=1D171=177N210=1I54=1I151=1X94=172N74=1I40=1I33=206N239=1I48=6183N154=4429N23=78S * 0 0 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCCTCACCAGCCCCAGGTCCTTTCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGAAGGAGACGCGCTGCTGCTGCTGTTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCTGGGGGTGGTGGTGGGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGTTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGCGAGCCGCCCTCCCGGAAGCCCCATATAAGAAACAGCGCCGCCACCTGTCTGGGTAGCAAGATCGGAAGAGCGTCGTGTAGAGATTGCGACCAAGTGT xIDO5V^}Iig[XcLWZTMVgVi`;Ffmoppppppppppoooi^foppppoonej+VYa\UM?3/.16>Q^ZTQOOQTW[_bddddaWNKNXbddb`][ZYYYTNLLMONFAAFLV^^\[\]`bddddddddddddddddddca^ZURONOV_dddddb_#_Fml20LUURYhTjXVxyEgy\YQrVxIcB6P~LU`kZ5UT>VmKS;SwAaXrSjRHaLMVWg6^yHZLO\[>H^]^4]aC\FvFXQa~~~~%Y\gBtbNa^h~WNm1^YbYnI]aln~0c~~~/Vb\sdmVi~6pCw[}QZ~KYb~N`Z~Me\w~N~Na~eG^t~SxJuRCpZsXoQkTZs~R~h~Pex_q~~~~5w~~B{evB{ZVqfuK:4KVd`M`f\xSMX|)s~VPheua^~6lkax_r[ecZb3X~Lw~6~a^e\r~~K[`j~~~~~}1v7pPMaiYYk~JXH~~~~'[^^ev~g~~Hp~,aCqLtbz\vbZZr^_^j[+P~_Cw6^u{3szM]}+0UNU&pNO}?_c~~~=^OP]~9_>JdqMKnbruf~}@gULUOT>PJNeMs~PdG\XNNdESWNanHrx~MfqLWVGlXbbH|}'i~M~f~T`w_eu~T\e[w_f\ibd\w~KufHx~8~gHjf\tbEVfUVNT^nN]c[oV%]e^w~Kvf^WXQ[rMYMJMAW~b~B~J|ff~Pe`A[rqxw9p`Sw^vS]{F]i~ToHx[vqd_rcqaq~S~l>jc~LaqP~Vt~{g-g[~AtLr]{U~~4t~|D_c[w~~CqM~b~TbYpJI0b>tfYlf[rfYPG|HP\upCL9;EMlU_f~N~FpS~?ur\Xkrp=~6e^~Md=Lu~rDf|vG\Ajnv~~?tfZMXXv=|Ptc_s|Ns_u~S\d\s~~s^;o~Ot{Sf_n~~+R\.Xsx{~+WyOQ?g8X_tc]l~-mx\~fes^s8Y=L[M[0tlK\w_~W\nRF;v_nbSed%r7r/OZj([bX~?[n~>wcs~RWP~M_~~~E^d^f~~~~?_~_WbwQ{~~>w~;U~NW2cNF{Wra^m^feeL~Om_e~`~BLp\[b~P`lC_q|QQFRS(_`~7Uk~Tuu~PsG]Yl_yex[gXr~;_^nOi~<[Z@Sw8][s~V_s_rjsc~T`^W[~U\t[k~~Ku}OufYgc~[~Hre\N\\_]r[cY{df[V3ZRcAtXpLbEZg,MaKZ~~EX_YWx9TvtM][set^m\ba~~~~d~Mn~~~~1p~8r~RjHcg_TCe]~e\gc[ss{KpeYK`Gf&^df0[?TMNc%UYX~E]xSc\cMv_s~xHJ@tex~9[bKaZW.*S[~1tJwAW~~DtZjfQ;V^lclb_'_e^qbEduf`s[[`i\P~4]~~EqpI~;\~~Eetb~@Yhc~Lr~~DYfFZ^z~|r,o~T^w~Kt~T~NvtuevfZ[Vn\wGr[kHn\ufhPa~hAg~q3MSex+dHu~Wc~:mU4~M~~:`5]w~CIcy=YYK}~~6eY~?i~Fuf~~3pZ_~W~DX\cBh~:|a\w]p7PvGk`~XbyQ[l[_q?\~c~@[b[ber`rct_~FamhbnPeZDho3pF^s~~~~3~Pcj~zAr\~h\ufX@E``PfBL^~~L\vdLtE[lf~SqTZ^^`Kd@MVXYq~@~~ZIE~7kh_rbI~P[_~Ouf[X~~L~~Ee^w_exy8Em~lb/]l7lb[gcfZo+p~SsvzOseu~K]~~~~:_ex\w[lf\X~U~QqYxEec_+S~~2_c~~Gbwe~H_tjuTsc~Msvr~hiLnf`p{(M]ao~'o~Arb[nGSE`CC|b~V`s]t~Sv`}5Vk[Go\^uu~L~J[PZ~feRge~~Axffux\u_Zt_~evH~`~=~Ks~~BvO~d~@tcuwKhbLJBug9xX_~S~;oSZn~;pxB@ob9p?Zc]b^<[?Lcp=pf\tchFacux~Mrft1]p~Ssc|?Z[Z]a^Zd\~T\rq~G\ug\w~~s>'>q4eBreNjZXvKrz&if]~A\_{[Dj`WpcsHXaIoEof.p6i~R~|DlMn~QN~R~~J\B~~~R~`~N{V?a{~X\l~plig~no~^l~~]~~\`[k~n~~M~~ntq~omlk~^l~^~~Ebgl~n~~~PRoa~~~~|~&~u~Lvp~rvt~G~k~~~~1rwpq~~]~~>clzYp}x1~?kj~Z~~Y[Ngn~]u@v~_m~qo~qm~Qr~E\}Q^n^l~F~~~S~~~^~JbT~g}qzqnft~n~~P~\k~~[R~M~~Rm~gEjq~~\qm~~~@~~\~~]~~P~~Erg{m}ji~~L~_lpT~M~q~r?~~_~Qo~sp~^L~cm~m~~~\Y|Ye{k~7Z\I~~Aj~Z{l~Tp~qdR~TZYl~q~l~tqZw~DupN~~J}sT~qf|^P~qQ~YB~~Nh8l~~ipqm~~\sbpv_fOzRfojkhb~s~\~_~sq~Vpx~pn~~$gen~X~_p~Qf_~0[T~mmTaq~akh~~_~~Snm~[t~T~[j~~~0gn~cv[~faj~~Jg~~JymC\~~M~~\bi|q~p~Z~o~pqqqo~gj~qm~pJQYyqp~~6~`~]x~D^iuH~Z~Y~]jpj~JR|%~[g_~CW]=qZc'^zj>d0Z\Nh{.8gjUe~oT~\}VXg~Mtq~~I~pmh~t=b2\s6c~T}kPur,c~X~~~~~6]~Y~o~j~m~g~~~8vnm~sqy_~\~n~iX|`}~7mlf~XQmy~UsfOe\i~~\~Q~S~~~@fsl~qmg~N~SW~Aqq~Vqr~~HWccr~~~~/o~jieh*~~~K~~O~kGgp~[C~fbnnthP]i~~Uppp~t~\p~ieE=U~~.Yk~Unqw~]qz~S~~~ZmJ~A~dm~~q~t~ctry~Zq~~^q}H~tKd~]~Tz~EFfft~~o~tgTth}Sn~o{~~@e}OYlm~p~v~_~mmgbj~m~Y~m~sqo~q~~~\wj~t~~~~.q~~a~~_a~Gl~]m~~Y~j~p~b~[xUy~~~?~mcdpIh]XU~~O~T~~hp~k~mzbq~~^~m~_~~~x~.~~\~~Z~jmtp|x~m~um|cn~~q~~FvKoqqr+{~D[`{Tk|adnlji@m~as4~mmw?~lillPm~p}~d~Njd~~~P~fm~~~~t3le^f~i4q[y~,k~jqqUm~~[fdy<^Y~_~~~Oo/bj~`_j\ipj~E~m~~q~\~Paymqn}h\z]P^m_XDf~j~tm~F~tl{~p XQ:Z:30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,45/50,30/32,44/46,0/0,0/0,26/26,0/0,42/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,42/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,52/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,52/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,42/46,0/0,0/0,26/26,0/0,50/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,44/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,32/32 SG:Z:G:0-15,VENUS:16-38,CBC:39-54,UMI:55-64,BOREAS:65-78,cDNA:79-1293,Poly_A:1294-1363,MARS:1364-1388 +read_rev_8 16 chr1 14400 18 98S194=1I236=140N69=757N108=1I44=659N159=92N198=177N87=1X48=237N74=78S * 0 0 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCTGGGGGTGGTGGTGGGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTTTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCCCCATATAAGAAAGAGGTGCCTCCCAGACTCTGTAGTGGAGATCGGAAGAGCGTCGTGTAGATCGGACCTGACAGAGT ~yqu~lr|J~l~~~\}~~|fZU~vhgtms~~~~~~~~~~~~~~~~~}xtdaht~x+Zq~~~}~~~~~~~~wmfcejt{}~||~~~~~~~~~ym`YYc~~&{k~~S~~~~~~w~~ag~~Zw~d~~~x~Xx~~~~a}uz~'i|l^~e~Xq~S~~{o~e~~h~{n~~~~E~~~r~H~~wrJj~[wo~Z~~~~~~~@~~~i~nSXot~W~~~Y}}qvb~~~~~Kf~~~U~xD~`b_{~f~M~~~av~d~l~m~w~\~~~~cth~~a~~~~Y~[i~m~~~f~yv~~~~M\B~Zj~~qRM~~~1{~~O~n~b~X~{jsa~g_~}b~~~~~p~~~b~~k~obilj~GyRd~~~{uzl~3r~i~~]~|a~|u~~ZTwoeu~~~~2~h~l{{zywO~]~l~sq~MukL~~~Y~_1o_`wux~U~~~~~bw~e~}~~~f~~z~_c~r~~~~~ny~]~~Y~v~s~c~~~Bq`iK~~~~t~zjhr~g~~U<[~\~fpdoCq~YkkHy~~S~~_}Y~~~~~V~~h]~^}~W~~Rphigjl~~~[n]}~l~`Zhhmg`~h~zf~\~~mh~\~~h~f~K[~~}v~z:Mu~~~Yb~U~n~OC}on~~d~v\wT~|sar~~~mzz}t~\~h~mj~tyc~~~~W~s~Jw~c|~^kg~v~Y~j~~~~t~qo~y~~~~h~Z~n~}~~^llp~~~~~Ku~z~i~_Z~\~~~^~a~t~~~~~~~~~~Ew~Rp~~g~~a~I~~~~Jym~e~W~~~a~~`~~~DHj}y~~@~~V~~~~~f~X~Nyp~~z~~~~~~v~h~~oygx~~fZq~h~~\~~~m~s~J~Kvk~~~~~J~^u~~k~bjt~~\f~~Z~tp~~~~:y~~vy~~W~]~clh~Jttb~Y~~cfw~f{B~~^~~Zb~~~~A~~aFl~gv=~~`ph~`~`uoxW_@Latpn~|^~b~|uc~~h~~j~~~~oli~~k~zo{w~n~[~v{Ai|~O~~mvW~p~]~_n~T^v~Xw~~~G`b~~~~~~B~~smZ~Y~~~S~~M~~[~p~h~~l~tjoyZq~~~hi~~~b~n~QL|~~/~~K~~~jyhs~by~~m~~~[~~~n~_wp~~~}~~~~z~U~~~kr~T~~Qg~m~g~~_~~~~~~~~k~~~y~Yr~qXrwBz~d~~~~~~\~1~q~r~t~~~y~y~Zlput~~~Ei}~}~~~~K~~~~~~6k_t~~hg~uT~~~~~K~~c~~~~~;qous~]Vs~~~~O~~~~Jc~v~~~n~h~\x~~Zs~~~~B~~Ov~apP~~~~~~c~^~~n~ru~~~e~f~~mr+q~jth}M~yUsnhc~~~~|~Xz|~~~z~~~~~~y~~or~t~b~~~V~sRxz~~~3~wwr~~J~~fp.~~~~~I~~~>ck~VfDzax~~M~}{t~g~~yy~y~X~~~~~~b~mZtnyf~~~~~~z~cYv~ch~Yr~~~~fuww XQ:Z:30/32,44/46,0/0,0/0,24/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,46/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,52/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,39/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,32/32 SG:Z:C:0-15,VENUS:16-38,CBC:39-54,UMI:55-64,BOREAS:65-78,cDNA:79-1295,Poly_A:1296-1370,MARS:1371-1395 +read_rev_9 16 chr1 14400 1 63S4=1I10=1I17=1X4=1X5=1I7=1X4=1X1=1X2=1I2=1X8=1X2=2D1=1D10=2X8=1D6=1I5=1D18=1I6=1I5=2I3=1X4=1D4=1X3=1I2=1I1=1X13=2I1=1X5=2I6=2I8=5I5=1X4=1I1X5=1X5=1I31=1X5=1X5=1X1=1X3=1D11=1X10=1X5=1I8=1D9=1D6=1I15=2I6=2I28=1X4=88S * 0 0 AAGCATGCGGGGTATCAATCCAGAGTACTTTTTTTTATGATTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTCTGCTCATGTTCTTTATTGATTGGTTTGCCATTTTCGTCTGGAAACCTCATCAGAAAGACAGTGGCTCACGGGTGGAGCCTCCCCCCCATGAGCACTAGGCAACAGAAGTCCCCGCCCCAGGCTGTGTTGGCCCATCAGGCCACCTTGCGCGTCTCATGAAGCTGGTCTCCGCGCACAGGTTGCTGGTTTTCCGTCACCTACCCCCCACCCAGGGGAAGCAGGTCTTGAGCAGCTTGTCCTGGCTGTGTCCATGTCATAGCAATGGCCCCAATCTGGTCTGGGGGGAAAGGTGTCATTGAGCCTCCCTACGATCCCAGTCGCCTCGTCCCTCCTCTGCCTGTGGTGCTGCTGAGCGGTGGCGGCAGAGGAGGGATGGAGTCAGACATGCCCCATAAAAGAAACCAATTCTTCCAACCAACACCTTAACTGCAGTGATCGGAAGTAGCCGTCGTGTAGATCTTCACAAGTAAGCT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:30/32,38/46,0/0,0/0,22/26,0/0,52/60,31/50,22/32,44/46,0/0,0/0,23/26,0/0,60/60,43/50,19/32,40/46,0/0,0/0,18/26,0/0,60/60,38/50,25/32,23/46,0/0,0/0,22/26,0/0,60/60,43/50,23/32,39/46,0/0,0/0,26/26,0/0,52/60,48/50,20/32,41/46,0/0,0/0,26/26,0/0,57/60,39/50,32/32,43/46,0/0,0/0,26/26,0/0,50/60,41/50,19/32,46/46,0/0,0/0,19/26,0/0,56/60,36/50,28/32,42/46,0/0,0/0,26/26,0/0,60/60,36/50,20/32,44/46,0/0,0/0,26/26,0/0,60/60,41/50,28/32,32/46,0/0,0/0,26/26,0/0,58/60,45/50,26/32,40/46,0/0,0/0,26/26,0/0,60/60,42/50,24/32,38/46,0/0,0/0,21/26,0/0,58/60,34/50 SG:Z:A:0-15,VENUS:16-45,CBC:46-61,UMI:62-71,BOREAS:72-85,cDNA:86-483,Poly_A:484-516,MARS:517-544 +read_rev_10 16 chr1 14404 15 175S426=140N69=757N110=85S * 0 0 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCAGCCACCCCATATAAGAAAGCATAGCGTTGTCTTTAACACTGCGCAGATCGGAAGAGCGTCGTGTAGAAGGCTCTGATCTAGGT ~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~$~~~~~~~~~~~~~d~~~~~~~~_~x~v~~~~~~k~~~~~b~~~~~~~~~~}~~~~~~~~~~O~~~~~~~~~~f~~pk\p@~~~~~~~<~~~~~~~~~~~1~~{~~~~~~~~~~~e~~~~m~~w~~~r~~n~~~~~~~~~~~~f~~~k~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~f~`~~~~{~~~~~<~~~E~~~~~~~~~~W~~~~~~~~~~~~~~~R~~v~~~~~~~q~~~~~~~~~~~z~~~~~>~~~~~~~~L~~~~~~~~~:~~~j~~~~~~~p~~~~~~`~~~~~~v~~X~~~~~~~~~y~~~~~~~~~~~~~~~~~W~~~~~~~~~~~~~~u~~~~~~~~~n~~~y~~~~~~~~~~~~~~R{~~~~~c~~m~~b~~r~~~[~~~~~~~~~~g~~p~~s~~~~~R~~~~~~~~~S~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~w~~n~~x~~~m~~~~~~t~~~~~~~~q~~~~s~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~a~~~~~~}~~r~~~s~~~~~~~~~~~~~~i~~i~~~~~~~~l~~~~~~~~~x~~~~~o~~~~~~~~~q~~~~~~`b~r~~~~~~~~v~~~~~~~~~~~~p~}~p~~b~~~~~~~~~~ XQ:Z:30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,44/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,56/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,54/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,52/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,50/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,54/60,48/50,32/32 SG:Z:M:0-15,VENUS:16-38,CBC:39-54,UMI:55-64,BOREAS:65-78,cDNA:79-689,Poly_A:690-839,MARS:840-864 +read_fwd_1 0 chr1 632482 1 69S3=1X3=1X3=1X1=1I18=2I48=1I1=1X15=1I1=1I2=5I4=1I1=1I3=1I3=1I4=3I4=1X1=2I5=2I4=1X1=2I1X3=1I4=1I2=1I7=1I6=1X4=1X6=1I5=1X2=1X1=1D8=1X17=1X5=199S * 0 0 AGAGTCCTAATACGCAGTCTACACGACGCCTTCCGATCTCCGGTATTGCAATACGCTGGGTGAATCCTATTCTTAAATTGGGAAAGCCTTCGCTTCGAAGCGTGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATAAAGGATGCCCCCCACCCGTAACGGTGGCACATCGATTACGATAGAATAGCCCGAAATTACATTAAAAAGCAACAGATCAAACAACAGGAAGGAAATCGACCCCCTCAAAGCGTGGTTCCATGCAACCCCAAGGCCTCCATGACTTTTTAAAAAATAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAGAAAAAAAAAAACAAAAAAAAAAAAAAAAAAATAAGAAAAAAAAAAGTACTCAGCTATGATACACTGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,10/26,0/0,56/60,42/50,27/32,35/46,0/0,0/0,23/26,0/0,56/60,40/50,23/32,41/46,0/0,0/0,17/26,0/0,60/60,31/50,22/32,35/46,0/0,0/0,26/26,0/0,58/60,35/50,20/32,40/46,0/0,0/0,24/26,0/0,50/60,41/50,18/32,35/46,0/0,0/0,26/26,0/0,58/60,29/50,22/32,34/46,0/0,0/0,26/26,0/0,56/60,39/50,22/32,41/46,0/0,0/0,20/26,0/0,60/60,34/50,13/32,39/46,0/0,0/0,24/26,0/0,58/60,35/50,27/32,40/46,0/0,0/0,22/26,0/0,60/60,34/50,23/32,41/46,0/0,0/0,19/26,0/0 SG:Z:F:0-16,VENUS:17-40,CBC:41-56,UMI:57-66,BOREAS:67-82,cDNA:83-299,Poly_A:300-480,MARS:481-504 +read_fwd_2 0 chr1 632508 1 83S22=1D13=1I16=1I2=1I11=1I11=9I6=1X5=1D7=1I33=1I16=2X20=1D17=267S * 0 0 ACCTCCCTCCCTCCAGAAAATCTACACGACGCTCTTCCGATTCTTGCGCAGCCATTGGTACCGTAGCCGTTTTTCTATATGGGGAAGCGAAAAGTCCTAATAGTAAAGAACCCTCCATAAAACCTGGAGTGACTATTACTGGATGCCCCCACACCCTACCACATGACAGCGACATTCTAAGAACCGTATATCATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCCAAAGCTGGTTCGAAGCCAACCCCATGGCCTCCTGACTTTTTCAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAGTACTCTGCTTTGATACCACTGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:32/46,0/0,0/0,26/26,0/0,58/60,48/50,26/32,43/46,0/0,0/0,21/26,0/0,60/60,44/50,21/32,32/46,0/0,0/0,21/26,0/0,46/60,44/50,30/32,33/46,0/0,0/0,26/26,0/0,58/60,47/50,28/32,34/46,0/0,0/0,23/26,0/0,54/60,44/50,26/32,33/46,0/0,0/0,17/26,0/0,50/60,42/50,24/32,36/46,0/0,0/0,26/26,0/0,60/60,43/50,27/32,38/46,0/0,0/0,20/26,0/0,54/60,40/50,27/32,25/46,0/0,0/0,26/26,0/0,58/60,45/50,25/32,46/46,0/0,0/0,21/26,0/0,58/60,35/50,17/32,46/46,0/0,0/0,26/26,0/0,58/60,44/50,17/32,35/46,0/0,0/0,26/26,0/0,56/60,45/50,28/32,42/46,0/0,0/0,26/26,0/0,60/60,32/50,25/32 SG:Z:D:0-19,VENUS:20-44,CBC:45-60,UMI:61-70,BOREAS:71-83,cDNA:84-272,Poly_A:273-521,MARS:522-546 +read_fwd_3 0 chr1 632510 1 84S19=1I11=1D6=1D4=1D20=1I1=1X21=1D7=1I14=1I25=1I13=1X16=1I11=1X6=1X1=1X2=1X1=1X5=205S * 0 0 AGTGTACAATTCAGCAGTCTACACGACGCTCTTCGCGATCTAGTCTTTCACCAAACGCGCGTTTATACCTGTTTCTTATAGGGGAGCGAAAAGTCCTAATAGTAAGAAGAACCCTCATAAACTGGGTGACTATATGGATGCCCCCACCCCCTACCACACATTCGAAGAACCGTATACCATAAAATCTAGACAAAAAAAGGAAGGAATCGAACCCCCCAAAAGCTGGTTTCATGCCAACCCCATGGCCTCCCATGACTTTTACAAAAAAAAATAATAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAGTTACTACGGCGTGATACACTGCT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,14/26,0/0,58/60,43/50,19/32,43/46,0/0,0/0,23/26,0/0,54/60,45/50,30/32,36/46,0/0,0/0,22/26,0/0,60/60,41/50,30/32,34/46,0/0,0/0,22/26,0/0,54/60,46/50,25/32,41/46,0/0,0/0,21/26,0/0,44/60,40/50,19/32,43/46,0/0,0/0,22/26,0/0,60/60,27/50,23/32,33/46,0/0,0/0,21/26,0/0,58/60,47/50,28/32,42/46,0/0,0/0,24/26,0/0,60/60,40/50,30/32,38/46,0/0,0/0,22/26,0/0,60/60,50/50,30/32,44/46,0/0,0/0,23/26,0/0,56/60,45/50,26/32,35/46,0/0,0/0,26/26,0/0,57/60,43/50,30/32,26/46,0/0,0/0,19/26,0/0 SG:Z:F:0-16,VENUS:17-41,CBC:42-57,UMI:58-67,BOREAS:68-84,cDNA:85-261,Poly_A:262-460,MARS:461-484 +read_fwd_4 0 chr1 632519 1 95S8=1I1X2=1D8=1I5=1I7=2X2=1I9=1X2=1X16=1I16=1I2=1D4=1X4=2I10=1I13=3I37=1I19=1X1=1X1=1X2=1X5=90S * 0 0 AGTGCGTTTTGCGAATTGTCTACACGATACCCTTCCGATCTCCAAGTTGCAAGTAGTACAGCACTGATTAGCGCTTTTCCTCTATATGGGACAGCTCCTAATATATAAAGAACCCTTCCATAAAACCTGACGTCGACTATATGTATTCCCCCCACCCTACCACAACATTCGAAGAACCCGATAACATCAAATGCCTAGACAAAAGAAGGAAGGAATCGAAAAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCGTCCATGACTTTTTCAAAAACAAAATAAAAAAAAAAAAAAAAAAAAAAAAAATGACAACTAAAAAAAAAAACAAAAACAAAAAAAAAAGGACTTCTAGTCGTGCGATAACCACTCTCGCACTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:28/32,40/46,0/0,0/0,24/26,0/0,57/60,40/50,27/32,36/46,0/0,0/0,26/26,0/0,56/60,42/50,22/32,29/46,0/0,0/0,26/26,0/0,54/60,35/50,22/32,43/46,0/0,0/0,20/26,0/0,58/60,43/50,28/32,28/46,0/0,0/0,23/26,0/0,46/60,39/50,30/32,28/46,0/0,0/0,26/26,0/0,44/60,34/50,24/32,37/46,0/0,0/0,19/26,0/0,52/60,28/50,26/32,41/46,0/0,0/0,22/26,0/0,54/60,44/50,26/32,34/46,0/0,0/0,20/26,0/0,57/60,20/50,24/32,40/46,0/0,0/0,23/26,0/0,57/60,32/50,30/32,35/46,0/0,0/0,26/26,0/0,46/60,39/50,14/32,36/46,0/0,0/0,18/26,0/0,54/60,35/50,22/32,29/46,0/0,0/0,26/26,0/0,48/60,27/50,24/32,29/46,0/0,0/0,19/26,0/0,32/60,38/50,23/32,28/46,0/0,0/0,24/26,0/0,36/60,23/50,18/32 SG:Z:I:0-17,VENUS:18-41,CBC:42-57,UMI:58-67,BOREAS:68-90,cDNA:91-272,Poly_A:273-345,MARS:346-380 +read_fwd_5 0 chr1 632563 1 79S11=1X4=1I17=3I17=1X11=1X14=1I4=1I19=1I1X5=1X1=1X6=1X5=1X2=1X1=1X1=1X6=97S * 0 0 ACTCGGTCAGGTCACGATCTACACGACGCTCTTCCGATCTGCTACCATCCGCAGTGTCAAGATCGATTTTCTGATATGGGGATGCCCCCCCCCCTAACCACACATTCGAAGAACCCCCCGTATACATAAAATCGAGACAAAAAAGTAAGGAATCGAACCCACCCATAAGCTGGTTTCAAGCCAACAACCATGCCTTCCATGCCTTTTGCATATATATATTAATAAAAATTTAAAAATAATAAATAAAAAATAAAAAATTAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAGTACTACTGCGTCTGATACCACTGCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:31/46,0/0,0/0,21/26,0/0,53/60,43/50,17/32,44/46,0/0,0/0,21/26,0/0,50/60,40/50,23/32,46/46,0/0,0/0,22/26,0/0,57/60,42/50,26/32,39/46,0/0,0/0,26/26,0/0,52/60,35/50,30/32,37/46,0/0,0/0,22/26,0/0,60/60,44/50,22/32,33/46,0/0,0/0,22/26,0/0,58/60,32/50,25/32,33/46,0/0,0/0,24/26,0/0,56/60,32/50,22/32,33/46,0/0,0/0,20/26,0/0,50/60,39/50,25/32,38/46,0/0,0/0,26/26,0/0,50/60,35/50,21/32,37/46,0/0,0/0,26/26,0/0,58/60,31/50,26/32,26/46,0/0,0/0,26/26,0/0,52/60,36/50,23/32,31/46,0/0,0/0,26/26,0/0,54/60,37/50,27/32,30/46,0/0,0/0,19/26,0/0,57/60,50/50,22/32,39/46,0/0,0/0,26/26,0/0,58/60,38/50,24/32,23/46,0/0,0/0,26/26,0/0,60/60,42/50,32/32 SG:Z:C:0-16,VENUS:17-40,CBC:41-56,UMI:57-66,BOREAS:67-80,cDNA:81-230,Poly_A:231-290,MARS:291-317 +read_fwd_6 0 chr1 632750 1 94S3=1X2=1X7=1I1=1X11=1I6=1I4=1X9=14I9=1D1=1X4=1D7=1X7=1D6=2I3=1X19=2X9=2I3=1X1=1X1=1D5=1I17=4I6=1I5=4I4=1X5=2I4=1X20=1D18=1I6=2I5=1X4=2X2=1X35=1D17=1X6=1D10=1D1X3=1X7=1I2=1I9=105I5=1X1=16I2X2=3I1=1D3=2I13=4I3=1D1X1=1X2=1X2=1I1=1X2=20I5=1I7=1I3=1D27=1I9=1D13=1X10=1I11=1X7=1X9=1D3=1X9=1D19=1D6=1D15=1D7=1X3=5I12=9I5=2D3=1D1X6=1I7=1X3=2X4=1D11=1X1=1I5=3I5=1I1=1I7=1X1=1D19=1D2=1X4=1X5=1X2=1X6=1X19=1X3=2I5=59S * 0 0 TATATGTGTATATCTGTGCTTACGCTTTCAGGCCGATCTACACTACCAACTTCCGTATCGGTCCACTAACCACAATTCAATGAATTGATTTCCTTATATTGATGGCACTAAGCAGCGCAAGTAAGGTCTAACAATACGCTACTTGCCACCCCCCACACCCCCTATCAATAAGACTTATCACCTTTCATATCACGCACCCACATAATCATTTTCCTTATCATCTTCCTAGTACCCTATGCCCCTTGTTCCTAACACTCACAACGAAAAAAACTGAACTAAATTATACAAACATGACTCACACGCTCAGGAAATAGAAACCTCTGAACTATCCTGCCCGCCCATCATCTCCTATTCCTCTTCCCCCTCCCATCCCTACGCATCCTTTACATAACAGACAGGTCAACGATCCCTCCCTTACCACAAATCAATTTCCACCAATGGTAACTTGAACCTACAGTAAGAAGGGGGTTGGGGATTGTGGAGTGTGAGGGGGGGGGGGTGGGGGGGGGGGGGGGGGTAAAGGGGGGGGGGGGTGGGGGGTGGGGGGGGGGGGGGGGGGGGAATATATATAGGGGGGGGGGGGGGGAAATCACGACGCGGACTAATCTTTAAACAAACATAAATAAGTTGGGGGGGGGGGGGGGGGGGCCCCCCAATTATTCACTAAACCAGGCGACCTGCGACTCCTTGACGTTTGACAATCAGTAGTACTCCCGATTGAAGCCCCTCATTCGTATAAAAATTACAACACAAGACGCTTGCACTCATGACTGTCCCCACATTAGGCTTAAAACAATGCAATTCCCGGACTCTAAACAAAAAAAATCCACTTTCACTGGGTGCATGCCTACAACCTGGGTATAACTACGGTCAAATCTCTAAATCTGTGGATCAAAACCACAAGTTTATCATGCCCAACTCCTAGAATTAATTCCCCTAATATCTATGAAAAAGAGCCCGTTTTTACCCTATAGCACCCCCACTAAGCCCCCACATAAGCCAAAAAAAAAAAAAAAAAAAAAAAAGTACACTGCGTTGTATACCACTGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:29/32,41/46,0/0,0/0,21/26,0/0,60/60,41/50,30/32,30/46,0/0,0/0,20/26,0/0,57/60,32/50,17/32,25/46,0/0,0/0,17/26,0/0,46/60,41/50,28/32,33/46,0/0,0/0,18/26,0/0,42/60,24/50,24/32,37/46,0/0,0/0,26/26,0/0,46/60,33/50,28/32,37/46,0/0,0/0,16/26,0/0,50/60,28/50,22/32,20/46,0/0,0/0,19/26,0/0,52/60,17/50,27/32,32/46,0/0,0/0,22/26,0/0,58/60,25/50,27/32,34/46,0/0,0/0,19/26,0/0,54/60,39/50,26/32,25/46,0/0,0/0,18/26,0/0,54/60,35/50,23/32,28/46,0/0,0/0,21/26,0/0,48/60,41/50,19/32,25/46,0/0,0/0,18/26,0/0,44/60,42/50,20/32,46/46,0/0,0/0,13/26,0/0,60/60,44/50,30/32,33/46,0/0,0/0,7/26,0/0,44/60,38/50,28/32,25/46,0/0,0/0,26/26,0/0,60/60,26/50,16/32 SG:Z:C:0-35,VENUS:36-61,CBC:62-77,UMI:78-87,BOREAS:88-102,cDNA:103-991,Poly_A:992-1024,MARS:1025-1050 +read_fwd_7 0 chr1 632756 1 77S38=1D26=1D1=1X24=1D4=1X15=1I3=1X2=1I1=1X1=1X6=1X2=1I6=1D13=1X4=1I28=1D11=1X7=1D9=1I10=1X8=502I7=382N3=1X7=1X2=1X3=2D22=2I10=1D3=1X6=1I9=1X2=1X3=60S * 0 0 AGAGGTCAATTCGCAGTCTACACGCGCTCTTCGATCTTGACAACCTAATATCGAGTGTATGGTCTTTTTATATGGGGAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTATTCCCCTATCATAGAAGAGCTTATCACCTTCATGATCACGCCCTCATAATCATTTCATTATCTGCTTCCTAGTTCCAGTCATGGCCTTTTACTAAACACTACAACAAAACTAATTAATGACTAACATCTCAGACGCTCAGGAAATAGAACCGTCTGAAATATCCTGCCGCCATCATTCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAAAGACGAGGTCAACGATCCCTCCTTACCATCAAAATACTCATGGTCAACCAATGGTACTGAATCCTCTGAGTACACCGACTACGGCGGGATAAGTTTCAACTCAACATACTTCACCCTCATTACTAACCTTAGAACCAGGCGCTTTGCGAACACAAATCCATAATACCCCCACCCTCTAACTACACCCAATCCACTCCCACAATACACAACCAACCCACCCTCACTAAATCACATCTCATTACCAAAACTTCCCAACCCCCCCTTCATCCAACCTTCCTACACCCCTCCACCCAACACCCTCACACCCTACATTATTATTCACCATCCTTCCACCCCCCCCCCCCATTCCTCCCCCCTTCTCTTACTTAACAACCCACCCCGCCCCCCCCCCCCCCCCCTCCCTAATTATATGAAAAAACACCCGCCCCCCCCCCCCCCCCTCGTCCAACAATCCCCCCCCCCCCAGTTTTCCGCCCCCCATCCATCTTCCTAGATTTTATTCCTAAAAATCTTTGAAATAGGGTACCCGTATTTACCTTTAGCACACCCCTCTACACCTTCTTAGCATGCTCATCAAAAAAAAAAAAAAAAATGTAAACTCTGCGTTGATATCCACTGACTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,10/26,0/0,54/60,34/50,21/32,29/46,0/0,0/0,22/26,0/0,46/60,40/50,15/32,37/46,0/0,0/0,26/26,0/0,46/60,43/50,25/32,40/46,0/0,0/0,22/26,0/0,60/60,40/50,25/32,35/46,0/0,0/0,22/26,0/0,50/60,39/50,22/32,36/46,0/0,0/0,21/26,0/0,34/60,38/50,21/32,35/46,0/0,0/0,22/26,0/0,57/60,36/50,27/32,36/46,0/0,0/0,26/26,0/0,36/60,33/50,24/32,39/46,0/0,0/0,23/26,0/0,50/60,36/50,27/32,39/46,0/0,0/0,20/26,0/0,34/60,27/50,19/32,40/46,0/0,0/0,15/26,0/0,44/60,33/50,27/32,38/46,0/0,0/0,17/26,0/0,40/60,48/50,16/32,37/46,0/0,0/0,22/26,0/0 SG:Z:F:0-15,VENUS:16-37,CBC:38-53,UMI:54-63,BOREAS:64-76,cDNA:77-898,Poly_A:899-928,MARS:929-957 +read_fwd_8 0 chr1 632756 4 102S8=4I15=2X33=1X6=1X1=2I11=2X3=1X3=2I1=1I5=7I9=1I12=1I6=1X4=1D12=1I6=1I22=2X35=1X21=1I1X9=4I4=4I6=1I5=4I12=1I1X7=2I13=10I1=3I2=3I3=1I8=4I9=1X10=1I5=1I3=1D1=1X3=1I3=1X1=3I2=2I2=1I7=1X11=8I16=7I7=3I5=20I2=3I7=3I5=4I3=1I8=1I6=5I10=100I8=1X6=10I7=4I22=1D2=1X2=1X1=1X3=1I4=1I14=1X2=1D9=8I2=1X13=2I6=27I7=25I2=11I9=14I1=4I5=3I6=1X1=1I4=2I6=1I3=1D4=1I3=1I20=4I7=1I3=1I12=1X6=4I7=6I28=1X3=280S * 0 0 AGTGCGTTGCGAATTGTCTACAACACGAAACCAGAAACGAACGCTCTTCTCCGATCCTCCATTCGTATCGTCCACAGTCCCTGGCTCGTTTTTCTTATATGGAATGGCACATATATGCAGCGCAAGTAGTCCTACAAGACGCTACTTCCCCTATCATAGAAGAGGTTATCAACCTTTTCATGATCAACCCCCCATCCATATCATTTTCAAGTTTCCTTATACTGCTTCCTAGTCCCTGTATGCCCTTTCCTAACACTACACAACAAAAACTAACTAATACTAACATCCAAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCAGCCCGCCATCATCCTAGTCCTCAATCGCCCTCGTCTCCATCACCCCCTACAGCATCCTTTCTTTACATAACACAACGAGGTCACAACGATCCCTCCCTAACCCCTATCCCTTGAAACCGATCAAATCAAGAAATTGGCCACCAATGGTACTCGAACCATACAGTACAACCAACCCCTAAACGGGCGGACAAATCTTCAACTAAACTCCCCCTACATACTTCCCCCCATAAATATTATTCACGCTAGACCCACAAACCGCCCAAAAACACAAGCAGGCGAACCCCTGCGAGAGACTTCCTTGACGGTTGACAATATAATCGAGTAGGTACTTCTTTATTCTATACTACTTTACTACCGCTCTCACTTTACTAACTCCCCGAATTGAAGCCCATAACTCTGCCATTGTACTTTGGTACTATCTCTACTACTCCCGATTGAAGGCCCTGAGCCCCCCCATTTAATCGTATAATAATTACATCACAAACTTCGTGCACATCATAGAGCTGTCCCCACAATAGCTTAAAAAAAAAAAACCATATGCAATTCCCGGGAACGTCTAACCAAAACACACTTTCATTCACCCACAAACCAATTCACCTCCATCCCAACTTTCCATCACCCGCATCAAAACACTTTCACATATTTCAAAACATTCACCGCTACAAAACGACCGGAGGGTAAATACTAGCGGCAATGGCTACTGAAATCTGTGGAGCAAACAACACAGTTTTCATGCCCCATCGTCCTAAAATTAATATTTTCCCCTAAAAAAAAAAATCTTTGAAATAGGGCCCGTATTTTCCCCCCCGTATTACAACCCTATAGCAAGATAGCACCCCCTCTATAAATCTCTCTACCGCCCCCCGCAAATCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAACAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTACTCTACTCGACTCTGCGGTTATACCACTTAGGCTT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:22/32,38/46,0/0,0/0,21/26,0/0,60/60,31/50,25/32,27/46,0/0,0/0,10/26,0/0,58/60,38/50,32/32,33/46,0/0,0/0,19/26,0/0,58/60,45/50,32/32,38/46,0/0,0/0,23/26,0/0,48/60,33/50,22/32,36/46,0/0,0/0,26/26,0/0,56/60,45/50,17/32,34/46,0/0,0/0,26/26,0/0,60/60,40/50,26/32,30/46,0/0,0/0,23/26,0/0,50/60,36/50,30/32,34/46,0/0,0/0,23/26,0/0,60/60,36/50,32/32,27/46,0/0,0/0,24/26,0/0,60/60,31/50,27/32,21/46,0/0,0/0,9/26,0/0 SG:Z:I:0-16,VENUS:17-58,CBC:59-74,UMI:75-84,BOREAS:85-103,cDNA:104-1197,Poly_A:1198-1371,MARS:1372-1408 +read_fwd_9 0 chr1 632757 1 81S21=1D42=1X5=1I9=2I8=1287I3=8D1=1X19=1X1=1I22=2I16=1I16=1X8=1I6=1I13=1I7=1I1X4=1X8=1X2=1X36=1I6=1D3=1X7=1X8=2I7=2I7=1X13=1D6=1I1X1=1X17=1X13=79S * 0 0 AAGGTCACCGGCACATTTCTACACGACGCTCTTACCGATCTTTGCTGCTCAAGCTGAGTTGCGTTTTATTTCTTATATGGGATGGCACATGCAGCGCAAGTAGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCAATGATCACGCCCCCTCATAATCATTTTCCCTATCCTCCATGCCCATTAGGCCCCTTCCTACCCCCCCTCACAACATACTACCCTATACTAACACCCCACCCTCAGACAACCTTCCCCCCCCCCCTTCCCCCCCCATCATCCCCTAGTCCCCTCATCGCCCCCCCATCCCCTACCCATCCCTTACATACACAGCACACCCTCCCCTTACCCCCCCCCCTCTCTCCCCATGCCACATGCCCCCCCACTCCCCTCTGCCCTCTCCACCCCCCCCCCTCCCCCCTGTCCCCCCCCCCTCCCCTGCCTCACTCCTAAAATCCCCTCCCTCCTGCCCCCCTCCCCTTTTCTCTCCTCTCTCCCCCCCTCCCCATCTAAATCCCTCCCCCCGCTTCCCCCTCCTTTCCTTCCCCCTTCTCCTATCATTCTCCCCTCCCACCTCCCCCTCATCCCCTCCCCCCCCCCCCCCCGCTCCCCCGCTCTCCTCCCCCTCCCTTGCCCACCCCACACTCCACCCCCCCCCCCTTTCCGCACTCCTCCCCTCCTCTGTTCCACTCCCCCACATGCCCTCGCTCTCTTCCTCCTTCCAATCCCTCCCCCATCCCCCCTCTCCCCTCCTTCCTGCCCCCCCCCCCCTGCTCAACTCACTCCTGTCCCCCCCCCCTCCTCCCCCCCCCCCCTCCCCTTTTTTTCCCCTCCCCCCCCCCCCCCCCCCTCTCCTCCCCCTCCCCCCCCCCCTCTTCCCCCTCCTCCTGGGTTTTTTTTCCTTCCCTGTCTCCCCTCTCCCCCCCCCTCCCCTGTTCCCTAATCTCTCCCCCTCCCTTCCTTCTCCTCTCCCCCCCCCTCCCCCTCCCTCCTCCCTCTCCTCCCTATCCCCTCCTTTCCTCCCCACCCTCCTGTTCACTGGCCCCTCCCCCCCTTCCCCCCCCCCTGTATCTGTCCCTCTCCTCTCCCCTCCTGAAAAAAAGTCCTTTTCCCCCCTCTCTCCTGCCCCCCCCCCCCCCCCACTCCCCCCCCCCTCACCTTCCCCCTCTTCCCCTCCCCTCCTCCCCCTTCCCCCCTCCCTCCTCTCCCCTCCCCTCCCCCCTCCCCCCCTGCCTCCTCCCTTTCCCCCCCTTGTCCCCCCCCCCCCTCCTCTCTTTCCCCCTCCCTCCCCCCACCCTGCTCTGCCCCTTCCCCCTTCTTACCCCCCCCCCCCCCCTCCCTCTTCTGCCCCTTATGCCCATCCCCCTGTTCCCCCTTCCACGCCCTCCCCCCTGCCCCCCCCCTCCCCCCCCCCCCTGTCTCTGCCCTCCTCTTCCTCCCTCTGCCCATCTTTCTGCTTCCTAGTCCTGTATGCCCCTTTTCCTAACACTCACAACCAAAAACTAACTAATACTAAACATCTCAGACGCTCTGGAAATAGAAAACCGTTCTGAACTATCCTCGCCCGCCTTTCATTCTAGTCCTCATAGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGGAGGTCACGTTCCCTCCATTACCATCTTAAATCAAATTTGGCCACCAATGGTACTGAACTACGAGTTCCACCGACTACGGCGGACCAATCTTCAACTCCCAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAGTACTCTGCGTTGATACCAACTGCTTATGAGTGGCTTCGAGGGA 8&-*979@2?279-';>.5.65&57:772%5:-$?070$636&76976:7>562$792,176);/#*46;'6=59:99??-%2?17:799778&377>56:8$*6::7>56:776::6=5???,:9:79::6>56966<50%69@1<>160%63$07:2(17::$:77.?4:78;>=/5,%%36%-%4&%$(&9$%&+%(03:9%;($(/%$('&%%$7'%($#'#$$)%$$'#'$($51%#'$$%###$6#2*&##""#5%&/)%%$%%$$%&$$'/'&-*&8%&75&)655#&&%-453#02&-%#,2'%5:$&48($$$&($#%484#7%$.%*$-$%##)$*#->(:???,<59=?/,,,,,,#+(+(+...%(),.'*))),.-----$*(+...%+(),..&+(+.')+,,,,,,,,#*.....$)*++,,,,,,,,#+...%)$/&+)*(+.&*+,,&*...%+..&+.&),.....$+...%)))((+(+.&+(+(*.-----$+...%(+(*,,&*..&*.....$-()(....%+.&))(.&)(....%))(+.&+)+))*)(+...%+..&*.&+....%+))+...%*,-------------#$(+....%-(+(+.&+....%+..&)(,..&*...%*)*(+.&#*,,,,,,,,,#))(.&-)*(+.&+...%+.&+()**(.'*(+....%*))),..&+(%(+(+()(.&+.&)(.',(*..&+....%(*.....$+(+...%+.&)(.&),+,,,,,,,,,,#),(+),)(+)*(+.&)*++,,,,,,,,#+.&+,,,,,,,,,,,#*...%()))))&-..%*+,,,,,,,,,,,,,,,,#+(+.&+....%*+,,,,,,,,,##()(....%+.&+.&)++')))))($&.&)(..&)*+(+...%+(++,,,,,,,#+...%)%+(..&+,(+(+(+....%$..&)(.&))(+.&+(++,,,,,,,#*....%+..&+.&+..&+(+.&+..&+)+...%+.&&$$.&+...%$..&+.&)**))*()+*...%*.-----$((+,,,,,,,,#)*+)+()*+..&+(+.&+(+...%+.&),++++++$*+.&&$(#-....$$(+(+.&),,-------------,#)(++,,,,,,,,#+)#.&)(....%+()(...%+...%+.&$....%)(.....$+..&+.&+(+...%+...%*.....$*.-----$),.&+.&+..&))'------$)(*+,,,,,,,,,,,#+.&+(+())(....%+..&*.....$*..&),(+(),...%)(....%))()(*,------------,#+..&+())(),...%)()),..&)*....%)**(....%)(.'*(,..&*.....$),+,,,,,,,#*,,,,,,,,,,,#)*#(+(),..&+.&+()(.&+..&+(),..&)+())((),()(.&+)*+.&)*+)),...%)))(.&+,))*(+)*),).'),,+%(+,)(+,(*+(*,,'))+(+)),*(-(+()+(+,&*),+,,&.&**((),,((+)+.&+(,..&-.&))())*)(+)%,.&+))*),..&+..&)+..&++(-))+.&))(+))*,))),*(+)),)+)*(**(..&+.'))(*.')+()(,,&*)+,&))'+*.'*.',(),)++(),,((++(,)**(.'*.&,*(++(+*(+)*.',(+())),)(+..%&***********************#(*++++++$*++(+()-(**(,)*+.',)(),()()),)*)+*())(,)++(+ XQ:Z:30/32,44/46,0/0,0/0,26/26,0/0,46/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,60/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,57/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,46/46,0/0,0/0,23/26,0/0,58/60,45/50,30/32,43/46,0/0,0/0,26/26,0/0,48/60,46/50,30/32,44/46,0/0,0/0,23/26,0/0,58/60,45/50,30/32,42/46,0/0,0/0,26/26,0/0,52/60,44/50,27/32,40/46,0/0,0/0,26/26,0/0,58/60,50/50,28/32,43/46,0/0,0/0,26/26,0/0,56/60,38/50,30/32,41/46,0/0,0/0,26/26,0/0,58/60,48/50,30/32,44/46,0/0,0/0,26/26,0/0,58/60,38/50,21/32,46/46,0/0,0/0,24/26,0/0,58/60,45/50,22/32,38/46,0/0,0/0,24/26,0/0,58/60,38/50,23/32,43/46,0/0,0/0,26/26,0/0,56/60,45/50,22/32 SG:Z:O:0-16,VENUS:17-41,CBC:42-57,UMI:58-67,BOREAS:68-81,cDNA:82-1737,Poly_A:1738-1768,MARS:1769-1794,P:1795-1812 +read_fwd_10 0 chr1 632757 1 80S9=1X12=2X4=1I6=1X8=2D19=1D1=1X3=1X15=1I9=1X1=1X13=1D7=1X33=1I9=1X40=1028I1X1=1X2=2X4=2D1X1=1D3=2D1X1=2D15=1X32=1D5=1D14=1X7=1X7=1I4=1D8=1X10=1I5=1D6=1X12=1I7=1D23=1X3=1X13=2D2=1I2=1X2=1D10=1D2=2X5=2X1=1X13=1I19=1D1=1X11=1I25=1D10=2X5=1I2=1I11=1I7=1X11=1D12=1D1=1X6=1X20=2I6=1X8=1I5=1X8=1X17=1I12=1X4=2X23=67S * 0 0 AACCCCGGACACACTTAGTCTACACACCTCTTCCGAACTGCAACTAGGTGCAGACAGAGATCTCTCTTATCTTATATGGGATGGCACATTCAGCGCAAGTAGTCCTACAAAGACGGTACTTCCCATCATAGAAGAGCTTATCACCTTCTTGATCACGCCCTCATAAATCATTTTTCCTATCTGCTTCCTATCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAAATACTAACCTCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCCAACAACGTAAAACGCCACGGGCCGCACTAAGCACCACGCAACCTAACCCACTCCCGCTGATGGCAAGACGATCTCCAACCCAGACTGTATCCACCGACAAAAAATACGAAACCCGCCGGTCATACAACTCAATGTCCCCCAAACCCCTTCCCAAACGCACCTTCGTCCAACCCGAGCCACCTACCTCCTCCAGAAATGGCTACGCACTTCTACAACTGCTCTCGGCCCACAAATCTCCCCACTCAAGCTACGCGAACTTCTCGAACTAGCCACATACTCCCTCCTGGCACACCCACGACAAGCCACTGCACACTCACATAACAAACCCAACCCACCACCGGCATACACAGGCATACAACCAAGCCCCCACGGATCGCATCCAGCAAAACCCGCGACATGAGCCTTCCGGCCCAGGGCACACGCATCCAGACGACCGCTACCTGAAGCAGCCCAACCACGCCCTGAGCTCCCTCCGCACCGTGACATATCATACGAGCGGGCCCCCTAGATAGAGGTGCCCACCCTCCAAGACAAATAAAATACCATCATACTGAAAAGAACCCACCCGTAACTACAACAGTCACCCCTCAACCCGGCCCCAAAACCACACAAGTCCATCGGAACAGACCACCCCAAACACCCTCCCCCACTAAACCCCCTACAAACGAGCCCCAAACAAACCCACGTGAAGAATCCGACCCAGTACCCGCCCCCCCAAGCCACGCCCACGTCCCTACACTAAGTATTACCCCCCACCGCCGTCACACAGACCGACTTACCTCAAACCGATGTGCCCACCGTTTAGCACCGCCTCCCCCAGCCGACAAAGGGGTCAGGAGATCCTAGTCCTCATTGGGGGAGTAAACGAGCGCCAAAAACCCCTTACGAGAAATGTGGGACAAGCTGAGTATGTCAGCAACCTCCATCATATTAGACACATACACCCCGGTTAGGAAAAGAAGGACCGAGGTACTAGGAGTTCTCCAGCAGGTCCGATATACCTACAGGACCAACGCAACACGAAATCAGTGTCGAGCCCTCCCATCCCTAAGCATCCTTTACATAACAGACGAGGTCAACGATCCTCCTTACCATCAAATCACTTGGCCACCAATGGTAACTGACCTACGAGTACACCGACTAACGGCGACTAACCTTCAACTCCTATCATACTTCCCCATTATTCCTAGAACCAGGCAACCGGCGACTCCTTGACTGAACCATGAGTAGTACTCCTATTGAAAGCACCATTCGTATAATAAATTACATCACAAGACGTCTGCACTCATGAGCTTGTCCCCACATTAGGCTTAAAAACAATGCAATTCCTCGACGTCCTAAAACCAAACCATCTTTCACCGCTACACGACCGGGGTATACTACGTCAATGCACTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATACGTCCAAGAATTAAATCCCCTAAAAATCTTTGAAAATAGGGCCCGGATTTTACCTATAGCACCCCCTCTACCCCCCTCCTAGAAAGCCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTACTCTGCTTTGATCCCACAGCT +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XQ:Z:0/0,7/26,0/0,56/60,43/50,30/32,39/46,0/0,0/0,26/26,0/0,56/60,38/50,26/32,32/46,0/0,0/0,23/26,0/0,56/60,34/50,23/32,37/46,0/0,0/0,23/26,0/0,60/60,40/50,30/32,46/46,0/0,0/0,16/26,0/0,58/60,42/50,27/32,32/46,0/0,0/0,18/26,0/0,54/60,48/50,22/32,35/46,0/0,0/0,21/26,0/0,60/60,39/50,30/32,37/46,0/0,0/0,22/26,0/0,60/60,42/50,23/32,39/46,0/0,0/0,16/26,0/0,60/60,39/50,17/32,43/46,0/0,0/0,26/26,0/0 SG:Z:E:0-17,VENUS:18-39,CBC:40-55,UMI:56-65,BOREAS:66-80,cDNA:81-1810,Poly_A:1811-1840,MARS:1841-1864